The invention provides a configuration circuit capable of completing FPGA re-configuration through user input and output ports. Through adding a user configuration interface circuit in a conventional configuration circuit structure, user input and output ports (user IOB) are connected with the configuration circuit, so as to provide conditions for the user input and output ports to access the configuration circuit and completing dynamic re-configuration. A bus interface circuit in the configuration circuit is improved, so the circuit is compatible to three operating modes of parallel configuration of the user input and output ports, parallel configuration of system input and output ports, and serial configuration. The configuration circuit prevents dependence on fixed system input and output ports, and FPGA devices can still change internal functions thereof after being built in a user system, so as to realize intra-system reconfigurability, and flexibility and reliability of a FPGA chip are improved.