The invention provides a element two-stage partition and twice polycondensation parallel method based on multiple document flows. The method includes the steps of firstly, dividing a finite element model into a plurality of initial sub-areas, and saving model information of each initial sub-area independently in a document; secondly, by each progress, simultaneously and independently forming a system equation of each sub-area, and performing polycondensation to remove internal freedom degree of each system equation; thirdly, by a local main process, forming packaging sub-area system equations, and performing polycondensation to remove internal freedom degree of each packaging sub-area system equation; fourthly, by the local main process, solving an interface equation, and solving the internal freedom degree of each packaging sub-area system equation by means of back substitution; fifthly, solving internal freedom degree of each initial sub-area according to results of the top packaging sub-areas by means of back substitution; terminating if iteration ends, or else starting again from the second step. On the basis of realizing distributed data storage, large-scale finite element parallel computing efficiency is increased by fully utilizing structural features of large-scale parallel computer systems by means of maximally realizing communication localization.