Something like this I haven’t tested it
get the environment
EnvDTE80.DTE2 pEnv = null;
Type myType = Type.GetTypeFromProgID("VisualStudio.DTE.8.0");
pEnv = (EnvDTE80.DTE2)Activator.CreateInstance(myType, true);
get the solution.
Solution2 pSolution = (Solution2)pEnv.VS.Solution;
get the project that you want
Project pProject = pSolution.Projects[0];
add the reference
pProject.References.Add(string referenceFilePath);