npm is like pip in Python, its a way to download and install packages. node_modules is a directory where these packages are installed. This is not the same as a virtual environment; which has the interpreter along with additional libraries.
In node, you can get a virtual environment (see: is there an virtual environment for node.js? for more details). The idea is the same - an isolated environment for better testing and portability.
In Python, there is requirements.txt (and pipenv), in node you have package.json (for packages), and modules (which go in node_modules).
The documentation goes into a bit more detail into the difference of these; but coming from Python you can think of a node package as something that has a package.json (so, like a setup.py), and a module is just any file you can import (or include() in node).