As per my understanding, one of the reason for slower simulink is because your model might include a MATLAB file S-function. MATLAB file S-functions also call the MATLAB execution engine at each time step. Consider converting the S-function either to a subsystem or to a C-MEX file S-function.
Refer to the documentation on Design Your Model for Effective Acceleration which helps to know about the techniques that you can use to speeduo model simulations.
