A low-cost, low-power and autonomous orbit determination system on chip for micro-satellites is proposed to solve the problems of high-cost, large-volume, high-power and low autonomous on traditional orbit determination systems. Using system on programmable chip (SoPC) as the hardware platform, and a 3-degree magnetometer with low power consumption is integrated in it. The state equations based on the satellite orbit dynamic equation are built and the observation equations with geomagnetic field vector are derived with the International Geomagnetic Reference Field (IGRF) model. The accurate output of position and velocity of micro-satellites are acquired by Extending Kalman Filter (EKF). To verify the feasibility of the system, a ground simulation system is designed with a magnetic simulator. Test results indicate that the system can reach the medium accuracy of micro-satellites orbit determination and can serve for micro-satellites with low position and velocity errors.