If you both are going to work on a shared codebase, the only sensible way is to use a language you both master.
The best option, by far, is to learn each others' language. Not only will this give you two shared languages to work with (which means you can choose the most appropriate one for the job at hand), learning new languages is essential to becoming a versatile developer with an eye for the big picture and a nice big toolbox full of alternatives to pick from.
Another option is to both learn a third language. This is especially interesting when neither language is a good fit for whatever it is you're going to build: both PHP and C# have some serious downsides, and it might just turn out that, say, Python could be the best language for your project. Again, learning a new programming language is always a good investment, even if you end up not using it.
A third option would be to strictly split up the codebase into a C# part and a PHP part, and define language-agnostic interfaces between them. For example, you could have a C# front-end that talks to a PHP server over a RESTful API. This is seldom a good choice, though, and it will make your team structure overly rigid: you can't just jump in and help with the other half of the project, because it's in a language you don't know. It also means the both of you will have a huge bus factor, so I suggest you don't do this.
TL;DR: Just get your act together and learn each other's language.