You could organize your files so that everything in subsection 1 is in the subsection1.1.tex file and each section and subsection has its own file. This would have the advantage of making the inputs clear in the main.tex file. Change the graphics path before each.
main.tex:
\begin{document}
\graphicspath{{Chapter1/}}
\input{Chapter1/section1.tex}
\input{Chapter1/subsection1.1.tex}
\graphicspath{{Chapter2/}}
\input{Chapter2/section2.tex}
\input{Chapter2/subsection2.1.tex}
\end{document}
I would recommend against naming files "section1.tex". Let LaTeX do the numbering. Name your files something meaningful, like "introduction.tex," and use labels to reference sections. Then if section 2 becomes section 3, you don't have to rename files.
directory structure:
Thesis/
thesis_main.tex
introduction/
introduction.tex
intro_sec1_filename.tex
figures/
figure1_name.png
figure2_name.png
theory/
theory.tex
theory_sec1_filename.tex
figures/
thesis_main.tex:
\documentclass[12pt]{book}
% List of packages
\usepackage{graphicx}
\begin{document}
% INTRODUCTION
\graphicspath{{introduction/figures/}}
\input{introduction/introduction.tex}
\input{introduction/intro_sec1_filename.tex}
% THEORY
\graphicspath{{theory/figures/}}
\input{theory/theory}
\input{theory/theory_sec1_filename.tex}
\end{document}
introduction.tex
% Introduction
\chapter{Introduction}
This is content in the first part of the introduction
\includegraphics{figure1.png}
intro_sec1_filename.tex
% Title of introduction section
\section{Title of introduction section}
This includes all of introduction section 1 content, including subsections
\subsection{Title of introduction section subsection}
This is the first subsection content
\includegraphics{figure2.png}
theory.tex
% Theory
\chapter{Theory}
This is content in the first part of the theory section
theory_sec1_filename.tex
% Title of theory section
\section{Title of theory section}
This includes all theory section 1 content, including subsections
figure1.png

figure2.png

/,./or../). Replace\input{foo}by\input{./foo}and the same for\includegraphicsas well. This speeds up file opening and more importantly avoids actual and future name conflicts with the system wide TeX files. – Jérôme LAURENS Nov 18 '21 at 12:47