The invention provides an on-orbit identification method for the stagnation position of the spacecraft sailboard two-dimensional driving mechanism due to rotation malfunction, the method comprises thefollowing steps: S1: determining through numerical analytical method, the practical solar vector Sm of the system, the theoretical solar vector Sb of the system and the analytical relationship between the pitching stagnation angle Theta and the yaw stagnation angle Psi of the sailboard; S2: calculating the analytical relationship obtained by the step S1 and obtaining two groups of solutions; S3:obtaining the information of the actual solar vector (the formula is shown in the formula) of the system by acquiring multi-point measurements and the information of the theoretical solar vector (theformula is shown in the formula) of the system through synchronous multi-point calculation, of which n is integer ranging from 2 to 200 referring to the number of the calculation points, and determining the true pitching stagnation angle Theta and the yaw stagnation angle Psi of the sailboard according to the minimum variance principle. The beneficial effect of this application lies in the measurement reliability and high safety degree, which provides a powerful engineering means for safeguarding the satellite energy.