The invention provides a microchip analysis system integrated capillary electrophoresis separation with chemiluminescence detection, which consists of a microfluidic chip, a single-path high voltage power source, a minipump, a three-way valve, an interface, a needle adjusting valve, a U-tube type monometer, a photomultiplier, a vacuum flask, an electric contact vacuum gauge and a time relay. The microchip analysis system provided by the invention has simple structure, no mutual interference of the capillary electrophoresis separation and chemiluminescence detection, and high separation efficiency of the capillary electrophoresis and high sensitivity of the chemiluminescence, has the characteristics of high separation efficiency, high detection sensitivity, small volume, light weight, convenient operation, low cost and the like, and is an ideal portable microchip analysis system.