The dual flow dependence set square root filtering assimilation algorithm comprises the following steps: S1, projecting a control variable in an EnSRF algorithm to an observation space to form a 4DEnSRF algorithm; s2, introducing a flow-dependent time window into a 4DEnSRF algorithm to form a DFD-EnSRF algorithm. The invention also provides a crop model remote sensing assimilation yield assessmentmethod based on the algorithm, and the method comprises the steps: T1, inputting meteorological data, crop parameters and soil parameters into a WOFOST crop growth model, and obtaining a simulated LAI set under the operation of different model parameters at a corresponding moment as background field data; t2, using DFD-EnSRF algorithm assimilation model to simulate an LAI set and an external observation LAI set to obtain an analysis LAI set; t3, aiming at analyzing the LAI set, obtaining the final assimilation yield through a SCE-UA optimization algorithm. The invention provides a new idea for improving the crop assimilation yield assessment precision.