According to the requirement of the assembly of a shaft and a sleeve for coaxiality, a coaxial positioning system was presented based on the flexible decoupling beams and micro-vision technology. To implement the online adjustments and maintain posture of the shaft and the sleeve, a flexible beam structure with a square pattern and two degrees of freedom was designed. Combined with a micro-platform and a clamp, this structure has achieved an exact coaxial precision in the positioning. According to mechanics, a stiffness model of the flexible beam was established. Then the parameters of the beams were determined by a simulation in finite element method. A micro-vision system was designed to be used in the system. Through the Hough algorithm, the precise coaxial positioning of the real-time detection was realized and the coaxial deviation computed was used as the value of the adjustment. Through lots of coaxial experiments, it shows that the coaxial positioning accuracy has been less than 8 μm. The results indicate that the positioning device can provide precise positioning of parameters, and can guarantee the realization of positioning assembly.