Function programmable circuit and operation method thereof

A function programmable circuit and an operation method thereof are provided. The function programmable circuit includes a micro-controller unit (MCU) and a field programmable gate array (FPGA). The FPGA connects to the MCU, which configures to execute a first function and works with the MCU in a first period, and the FPGA is being programmed a second function by the MCU at the same period. Wherein the FPGA is controlled by a function switch pulse output from the MCU to end the first period and switch the first function to the second function, and executes the second function and works with the MCU in a second period.