The invention relates to a serial port instrument monitoring system and a debugging method thereof. The system comprises a mode selecting module, a monitoring module, an independent data direction indicating module, an independent power supply module and a peripheral interface module, and the monitoring module is respectively connected with the mode selecting module, the independent data direction indicating module, the independent power supply module and the peripheral interface module. The debugging method comprises the steps that first, equipment connecting is carried in series and in parallel, a terminal is opened for connected line detecting, if detecting is successful, loop detecting is carried out, otherwise, returning or reconnecting is carried out, then loop detecting is carried out, and if loop detecting is not successful, returning or reconnecting is carried out; and after loop detecting is completed, according to specific using requirements, the mode selecting module is arranged to have a data taking or instruction taking function, and data collecting or instruction capturing is achieved. The problems that instrument equipment is detached repeatedly, so that data transmission reliability is lowered, and data monitoring or instruction capturing operation is complex are solved, and convenience and easiness of instrument or working industrial intelligent computer instruction monitoring are achieved.