Will I be able to use the raspberry pi with node.js to control something connected to the pi with a website with wifi. And also will it be the same as php or will it have limitations
Without knowing anything specific about what you are trying to achieve, I would say yes, no problem. I do it all the time. For example a simple NodeJs WebServer that serves a webpage, including a WebSocket Server to receive real-time commands or via REST API. Almost anything is possible.