How to join two or more external .tex file using another .tex file and then compile?

As a best practice, I arrange your scenario as follow to be more general. You have:

• a package mypackage.sty in which you put all packages used in both main input file and sub files (child files).

  % mypackage.sty
  \NeedsTeXFormat{LaTeX2e}[1994/06/01] 
  \ProvidesPackage{mypackage}[2013/05/01 v0.01 LaTeX package for my own purpose]
  \RequirePackage{amsmath}
  % put other packages here
  \endinput
  

• the first input file input1.tex as a sub file (child file) as follows. It loads mypackage.sty package.

  % input1.tex
  \documentclass[preview,border=12pt]{standalone}
  \usepackage{mypackage}
  \begin{document}
  Karl's students do not care about arrow tips.
  \[
  E \ne mc^2
  \]
  \end{document}
  

• the second input file input2.tex as a sub file as follows. It also imports mypackage.sty package.

  % input2.tex
  \documentclass{article}
  \usepackage{mypackage}
  \begin{document}
  Karl's students do not care about dashing patterns.
  \[
  pV = nRT
  \]
  \end{document}
  

• the main input file main.tex as follows. It must load mypackage.sty and docmute packages. docmute package is used to import all stuffs (of the imported sub files) inside \begin{document} and \end{document}.

  % main.tex
  \documentclass{article}
  \usepackage{mypackage}
  \usepackage{docmute}
  
  \begin{document}
  \input{input1}
  \input{input2}
  \end{document}
  

The following simulates your scenario. Compile it with -shell-escape.

\documentclass{article}
\usepackage{filecontents}

% creating a package
\begin{filecontents*}{mypackage.sty}
\NeedsTeXFormat{LaTeX2e}[1994/06/01] 
\ProvidesPackage{mypackage}[2013/05/01 v0.01 LaTeX package for my own purpose]
\RequirePackage{amsmath}
% put other packages here
\endinput
\end{filecontents*}

% creating the first input file
\begin{filecontents*}{input1.tex}
\documentclass[preview,border=12pt]{standalone}
\usepackage{mypackage}
\begin{document}
Karl's students do not care about arrow tips.
\[
E \ne mc^2
\]
\end{document}
\end{filecontents*}

% creating the second input file
\begin{filecontents*}{input2.tex}
\documentclass{article}
\usepackage{mypackage}
\begin{document}
Karl's students do not care about dashing patterns.
\[
pV = nRT
\]
\end{document}
\end{filecontents*}

% creating the main input file
\begin{filecontents*}{main.tex}
\documentclass{article}
\usepackage{mypackage}
\usepackage{docmute}

\begin{document}
\input{input1}
\input{input2}
\end{document}
\end{filecontents*}

\usepackage{hyperref}
\begin{document}
\immediate\write18{pdflatex main}
please open \url{main.pdf}
\end{document}

Notes

Some people use the combination of standalone document class and package. And some other people use the combination of subfiles document class and package.

But I believe my method above is much more flexible than these two methods because the included input files can make use of any document class.

I would recommend the standalone package:

Notes:

• The geometry package was used to change the paperheight so as to make it easier to show an image here.
• The color was used to make it easier to see the content fro the different files.
• The filecontents package was used to package the separate files into one MWE .

Code:

\documentclass{book}

\usepackage{standalone}
\usepackage{xcolor}
\usepackage[paperheight=12.0cm]{geometry}

\usepackage{filecontents}
\begin{filecontents*}{file1.tex}
    \documentclass{book}
    \begin{document}\color{blue}  
        \chapter{Chapter-1}  
        \section{Section-1}
        Text from File 1.
    \end{document}
\end{filecontents*}

\begin{filecontents*}{file2.tex}
    \documentclass{book} 
    \begin{document}  \color{red}
        \chapter{Chapter-1}  
        \section{Section-1}
        Text from file 2.
    \end{document}
\end{filecontents*}


\begin{document}
\input{file1}
\input{file2}

\color{brown}
\chapter{Main File}
Text in main file.
\end{document} 

use the documentclass combine if you want to create a new document which combines several other TeX documents. Run texdoc combine to get the documentation for combine