Hello 260068845@qq.com,
So, basically you want to disable the default step interrupt and have an etimer interrupt every 200Hz (btw, 200Hz is 5ms not 500us). An easier approach is to use the PIT timer, the one used for the step timer function.
However, I have attached a model that uses the eTimer to provide an interrupt every 200Hz that toggles the PA1 pin (scope channel 2 - in the image attached). On the PA0 there is the OFLAG output of the eTimer that is changed whenever the COMP1 and COMP2 registers are swapped together. If you need to trigger the signals every 2kHz, you need to compute other values for the Primary counter input source (Prescaler) and the comparator initial values.

Hope this helps,
Marius