Hello lijiantaowy@163.com,
The Timer options selets the Step Tick peripheral. If you select the PIT Channel 0, the toolbox automatically configures the Pit peripheral to trigger an interrupt every step time set in the simulink configuration, in your case 0.001s. What you are facing with the FreeMaster interrupt is normal, those interrupt requests come at higher frequencies. As am example, you can compare timings from our Motor control examples in our toolbox.
When select the Timer as Supressed, this means that the toolbox will not trigger automatically the step function, so you will need to add a timer interrupt, and inside it to put your model. Right now, when you select Supressed this means that probably your app is not even running right now.
Hope this helps,
Marius