Cross referencing between chapters in thesis (LaTex)

There are several packages that would do the job. I would recommend to use the hyperref package in combination with the cleveref package. hyperref should be loaded last and cleveref afterwards. The former one enables the base functionality for hyperlinks and the latter one extends it (it automatically determines the type of the referenced object and will precede the number accordingly with equation, table, figure). Then assuming you labeled your equation you can simply reference it with cref{eq:label_of_equation}. The eq: is not mandatory but it helps in keeping the overview.