Make the bibliography as a section in each included chapter

I would post this as a comment but I don't have enough reputation (yet!).

Have you seen this question? Automatically split sources list into bibliography and references It appears to do what you're after.

Essentially using that answer with your MWE, your document would look like:

documentclass[12pt,a4paper]{book}

usepackage[utf8]{inputenc}
usepackage[T1]{fontenc}
usepackage{amsmath}
usepackage{amsfonts}
usepackage{fancyhdr}
usepackage{amssymb}
usepackage[dvipsnames]{xcolor} 
usepackage{booktabs}
usepackage{decorule}
usepackage[french]{minitoc} 
usepackage{hyperref}
usepackage{filecontents}   % only for MWE
usepackage[language=french, style=authoryear, sorting=none, backend=biber, bibencoding=utf8, natbib=true, citecolor=gray]{biblatex}
mtcselectlanguage{french}

% adapted from:
% https://tex.stackexchange.com/questions/495194/automatically-split-sources-list-into-bibliography-and-references

% hyperlink setup
hypersetup{
    colorlinks=true,
    linkcolor=blue,
    citecolor=gray,
}

% just used for the MWE.
begin{filecontents}{biblatextest1.bib}
@book{cite1,
    author = {Baker, M.},
    year = {2010},
    title = {The book},
}
end{filecontents}
%
begin{filecontents}{biblatextest2.bib}
@book{cite2,
    author = {Smith, E.},
    year = {2008},
    title = {The other book},
}
end{filecontents}

addbibresource{biblatextest1.bib}
addbibresource{biblatextest2.bib}

% Append keywords to identify different bibliography entries.
% Add a map for every chapter, so that the bibliographies are kept separate.
DeclareSourcemap{
    maps[datatype=bibtex, overwrite]{
        map{
            perdatasource{biblatextest1.bib}
            step[fieldset=KEYWORDS, fieldvalue=ch1, append]
        }
        map{
            perdatasource{biblatextest2.bib}
            step[fieldset=KEYWORDS, fieldvalue=ch2, append]
        }
    }
}

% change bibliography from chapter to section
defbibheading{bibliography}[bibname]{section{#1}}

begin{document}
    
    tableofcontents
    
    %setcounter{mtc}{5}
    part{titre de la partie 1}
    % This goes in your Chapters/Chapter1.tex file
    chapter{Chapter 1}
    section{Introduction}
     Text cite{cite1}.
         
    cleardoublepage
    addcontentsline{toc}{section}{Références}
    printbibliography[title=Références Ch1, keyword=ch1]
    
    %setcounter{mtc}{6}
    part{Titre de la partie 2}
    % This goes in your Chapters/Chapter2.tex file
    chapter{Chapter 2}
    section{...}
    Some more text cite{cite2}
    
    cleardoublepage
    addcontentsline{toc}{section}{Références}
    printbibliography[title=Références Ch2, keyword=ch2]

end{document}

To briefly explain what's going on, you have a separate .bib file for each chapter of your thesis, and reference each text within each file as normal, ensuring that all of your citations in each chapter refer to one file only.

You then display each file at the end of each chapter, using the keyword mappings set up in the preamble.

Some things I've adapted:

• In the printbibliography command, you can specify a title.
• I've used the hyperref package to give you hyperlinks, and made them blue.
• Since printbibliography comes with its own title, I'm adding a reference to it in the table of contents with addcontentsline so that you don't have a blank page in between both.

I'm not sure how to adapt this to use one .bib file only, sorry. Good luck with the rest of your thesis. :)

Your TOC has separate references:

and each reference list is unique: