In order to solve the deficiency of one-dimensional auto-focusing technology, on the basis of the Six Degrees of Freedom (6-DOF) platform, a three-dimensional auto-focusing system is proposed based on the image processing technology. The system utilizes the CMOS as an image sensor, and the 6-DOF platform as an actuator, and a computer for obtaining image definition evaluation value and driving 6-DOF platform to realize three-dimensional auto-focusing. The auto-focusing experiments have two parts, which are one-dimensional and three-dimensional auto-focusing closed-loop. According to the coupling relationship of the X-axis, Y-axis and Z-axis, a modified Stochastic Parallel Gradient Descent (SPGD) algorithm is presented. The experimental results show that the closed-loop error is below 3 percent, which meets the precision requirements for three-dimensional auto-focusing.