How to accurately measure 16MHz clock with Oscilloscope

@KevinWhite has given the correct solution.

Analysis. The underdamped square wave indicates peaks every 2/5 in 1cm at 50ns per cm=division approx. thus 40ns cycle = 25MHz resonance. This is common with long ground lead inductance 0.5~1nH/mm and special coax used in 10:1 probe < 90pF/m. The computed resonance is dependant on the length of the ground lead inductance. Thus to expect an increase in resonant frequency requires better impedance matching of the probe 10RC+L : 1RC ratio by reducing the L value. This raises resonant frequency by inverse square root (LC), so to raise 25MHz to 200Mhz 1:8 requires reducing the ground lead length by a factor of 64 down to ~5~10mm from (est. = ) 160~320mm supply or ground lead length including probe ground path length on cct board gnd location. So I predict your probe ground lead was too long and also calibration imperfect.

Conclusion: use ground pad or test points directly at IC. Ensure Vdd,Vss is decoupled by at least 10nF directly at IC. As these also add path inductance to Zout.

Also consider CMOS output impedance ~ 50 Ohm +/-50% from RdsOn is also mismatched and further improvement can be made by examining all stray loads of breadboard wiring to output. (L,C)

P.s. 25MHz probe resonance is pretty common and this is another reason why all DSO’s have 20MHz LPF with amateur 10:1 probes.

Your oscilloscope photo indicates that you are able to measure the MCU clock at 16 MHz quite nicely.

You should be using a "10X" probe. It will add some capacitance to the MCU oscillator, which will likely shift its frequency lower. If the MCU oscillator has an input pin and an output pin, probe the output pin.

Your OWON oscilloscope has a time-base accuracy of $pm100$ parts-per-million. If you need more accuracy, measure frequency with a frequency counter instead...a decent frequency counter should contain a more accurate time base.

Your OWON 'scope has an internal counter claiming 6-digit resolution. If this internal counter uses the main timebase (having accuracy of 0.01%) then its least-significant digits are suspect.

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From the OWON SDS1102 manual:

Counter:
It is a 6-digit single-channel counter. The counter can only measure the frequency of the triggering channel. The frequency range is from 2Hz to the full bandwidth. Only if the measured channel is in Edge mode of Single trigger type, the counter can be enabled. The counter is displayed at the bottom of the screen. Operation steps:

• 1.Push Trigger Menu button, set the trigger type to Single, set the trigger mode to Edge, select the signal source.
• 2.Push the Acquire button to show the right menu.
• 3.Select Counter as ON or OFF in the right menu.

The shape of the waveform won't affect the fundamental frequency of a signal. However an oscilloscope is usually not the correct instrument to accurately measure frequency. It may only have an accuracy of 1% or so.

As @glen_geek points out in his answer some oscilloscopes do have counter/timers built into the instrument that can give high-accuracy (typically only for a single chanell) but the frequency displayed using the normal measurement facilities are usually only obtained after the signal is sampled and so will not be as accurate.

If you want to measure the frequency accurately and your scope does not have a built-in frequency counter you will need a frequency counter/timer such as [Keysight 53230A 350 MHz Universal Frequency Counter1

The wave shape distortion you see is almost certainly because of your probing technique. The probe should have an extremely short ground - a couple of inches is too long. Your oscilloscope probe accessories will probably contain some small springs that are used for this purpose.

To get the best waveform I don't use a probe and instead use coax wired directly to the signal. with very short connections.

If the source cannot drive a coax cable directly a 470 or 910 ohm resistor at the probe point can make an ad-hoc 10:1 or 20:1 attenuator with very good frequency response (up to a few GHz). Set the oscilloscope to 50 ohm input impedance if using this approach.