By default, Simulink uses 'normal mode' to simulate a reference model. Normal model means that the model is simulated similar to a subsystem type model.
Another simulation mode for reference model is 'accelerator mode'. Here, a code is generated for the reference model and is then compiled into an executable format. In this mode, the simulation speed will increase compared to the original model.
You can set this option by doing:
1) Right-click the model block and select Block Parameters.
2) Set the simulation mode to 'Accelerator' and click OK.
Note that when doing this, some time is taken to generate code for the reference model. The code is generated when the reference model has changed, not for every simulation.
Hope this can help to solve your question.