Light path of an alignment system based on four-quadrant photo-detector is analyzed. The determination for input-output characteristics of the system is transformed as calculating the illumination area, and the calculation method for every quadrant is given. The mathematic model of the system is given. Simulation results show that the linearity of input-output of the system is different for different parameters of “m shape” sign. And there exists a set of parameters, with which the input-output characteristic of the system is linear. Measurement results show that both maximum align and measurement errors are less than 2 μm, which proves that the model is correct, and the alignment system can be extent to micro-displacement measurement from alignment. With this work, dull calibration work and nonlinear error can be avoided, and both efficiency and accuracy can be improved.