A method and device for estimating spatial distribution of power system inertia based on multi-innovation identification. The method includes: (S1) acquiring time-series data including each node frequency of a power system and a transmission power of a transmission line; decomposing a frequency signal in a series of different spaces to identify a disturbance occurring moment; (S2) analyzing a relationship among node inertia, node frequency and node injection power; constructing an OEMA model to describe an active power-frequency dynamic process of the node after the disturbance occurs; analyzing a coupling relationship between an unknown parameter of the model and the node inertia; (S3) solving the OEMA model based on multi-innovation identification to identity the unknown parameter; and (S4) according to the relationship between a vector of the parameter and the node inertia, calculating each node inertia to estimate the spatial distribution of the power system inertia.