I tried to build a new theme for nopCommerce Shop, I found there's a style.css file which controls the style of the websites, but where's this file being cited in the webpage?
Any style sheets added to your theme folder are added automatically at runtime. All you need to do is create your theme folder, make your css changes and change the theme in web.config <pages theme="YourTheme">
In nopCommerce 3.0 or newer version, if you intend to keep most of the theme and just supply your own style.css, open up Themes\<theme name>\Views\Shared\Head.cshtml, and modify the following line of code