The invention relates to the aerospace field and is a sparse measurement method for a complete spatial baseline VLBI system. The purpose is to reduce the burden of data acquisition, storage and communication when the spatial VLBI system is used for spacecraft orbit measurement by the sparse measurement of VLBI signals. The method is as follows: according to the VLBI measurement principle, constructing the measurement model of the complete spatial baseline VLBI system, and giving a delay calculation method; further according to the sparse prior characteristics of the spacecraft orbital parameters, designing the sparse measurement mode of the spatial VLBI navigation signals, and establishing the sparse sampling and reconstruction method of navigation measurement signals. This method can significantly reduce the scale of VLBI measurement data, and provide reference for the constellation configuration design and data processing of the complete spatial baseline VLBI system.