To promote the efficiency of microarray gene chip images scanning and acquiring,a microarray fluorescent spots images scanning system is developed,in which an epi-fluorescence microscope,a precision three-dimensional (3D) translation motion platform,and a thermo electric cooling CCD camera are integrated effectively to construct an imaging and scanning mechanism. This system utilizes the industrial personal computer (IPC) as the core of measurement and control and realizes three specific functions,such as microscope auto focusing control,fluorescent spots images auto scanning and sampling and microarray spots images stitching. Many assays and experiments have been preformed to manifest that the system can effectively promote the efficiency of the microarray polymerase chain reaction (PCR) experiments and analysis.