The invention discloses a remote serial port debugging method and a system thereof which are applied in the field of equipment debugging, wherein, the debugging method includes the steps of: establishing a serial port channel between a control terminal and a debugging terminal; outputting a serial port channel testing instruction by the control terminal to the target board at the debugging end tocheck whether the serial port channel is unimpeded; if yes, sending the debugging instruction by the control terminal to the target board through the serial port channel and carrying out debugging operation on the target board. The technical proposal provided by the invention can realize remote equipment debugging without needing to modify the level software drive, thus simplifying the procedure of remote equipment debugging, further saving unnecessary development of debugging software, and increasing the capability and scope of remote debugging; meanwhile, the implementation of the technicalproposal will not affect the stability of single board and the current business functions.