Bias registration is an essential process for correcting the system bias of sensors. In order to estimate the sensor system bias without cooperation targets a three-dimensional bias registration algorithm was proposed based on linear Kalman and least squares. This algorithm takes the curvature of the earth into account and can estimate the system bias of elevation angle that cant be calculated with the traditional 2D method. The system bias of sensors and the motion of target are combined into the same measurement equation by constructing a system model. Then the estimation of system bias is completed by using the linear Kalman and least squares. Simulation results show that system biases can be estimated effectively including elevation angle bias.