The invention relates to a chip electrophoresis special programmable power supply system, which belongs to the electronic information technical field. The invention solves the problem that the prior power supply control system fails to simultaneously have the functions of a wide voltage range, a lower current density, multiple outputs, etc. The invention which adopts a twin-CPU programmable power supply structure consists of an upper PC machine, a monitoring human-machine interface connected with the upper PC machine, a lower MCU, multiple D / A switching circuits connected with the lower MCU, a power supply module respectively connected with the D / A switching circuits, an A / D switching circuit connected with the lower MCU, and a serial communication circuit arranged between the two CPUs of the upper and lower machines. The chip electrophoresis special programmable power supply system is characterized in the program control of multiple DC voltage outputs, the high accuracy of voltage control and data acquisition, high stability, multiple chip electrophoresis program control modes, real-time display of testing curves, data and curves storage, data inquiry, etc. The programmable power supply system is applicable to a plurality of operational modes in single-dimensional and multi-dimensional, etc. of chip electrophoresis and has applications in biochemical analysis based on electrophoresis separation, etc.