The invention belongs to the field of spacecraft control, and relates to a fault mode thrust allocation method for a geostationary orbit satellite electric thruster. The method comprises the steps of firstly, determining a thrust allocation input condition, including ignition position constraint, ignition velocity increment constraint and orbit control demand; secondly, allocating and optimizing position keeping thrust, establishing an electric thruster pointing model, selecting a thruster, defining ignition parameters, and optimizing and calculating the ignition parameters; and finally, calculating an angular momentum unloading deflecting vector. Aiming at the problem of high fuel consumption in a traditional definitive solution mode, a nonlinear hybrid constraint optimization model is established, and key parameters such as time length of each thrust ignition arc, ignition position and the like are solved by taking fuel optimization as a target, so that the method can realize fuel optimization under engineering constraints.