The technique of the load identification of mass variable system was studied. The generalized modal concept applied on time varying system was introduced, and the method of modal superposition was used to give dynamic equations with partially decoupled in initial modal space defined at initial instant. Based on both virtual distortion method (VDM) accounting for the effect of mass change and the Duhamel integration in initial modal space, two approaches to identify modal forces were constructed: one is the recursive calculation pattern formulated on the basis of modal acceleration, and the other is the regularized solution by the direct discretization of Duhamel integration with modal displacement and acceleration. A mass variable system with 16 degrees of freedom subjected to two external loads was analyzed. The responses were calculated by applying Euler midpoint symplectic difference method and added with random noise to simulate measured signals. Two dynamic loads were identified by two inversion approaches of modal forces. The comparison of results has indicated that regularized solution format has a higher numerical robust than the recursive calculation pattern, but the latter is sensitive to the noise of measurement.