How can I know the performance of the MCU?

Unless you put it into a "sleep" mode, the CPU usage is always 100%

If your processor has nothing else to do but the FFT, then the FFT will consume 100% of the CPU cycles until it's done.

"Is there any method?"

If you're using an RTOS, read its documentation to find what facilities it provides.

Otherwise, toggle an output pin at the start of the FFT, and again at the end - and observe it on an oscilloscope.

Or look at www.keil.com/.../uv4_db_dbg_execprofiler.htm