The invention discloses a block adaptive type Cartesian grid rapid graph mapping method and system, and the method comprises the following steps: S1, after an MPI environment is initialized, importing geometric data of a distributed block adaptive type Cartesian grid into each processor so as to reconstruct a multi-way tree structure, and building a link relation of adjacent hierarchical nodes; S2, sharing node geometric information at a region decomposition boundary across processors, and storing the node geometric information in a corresponding virtual node data container; S3, constructing a local geometric topology of each leaf node on the current processor; S4, normalizing the completely overlapped geometric elements on each processor; S5, based on cross-processor query operation, establishing dynamic communication mapping of docking surface elements at the region decomposition boundary; and S6, exporting the non-structural polyhedron computational grids in parallel on each processor. The problems that in the prior art, a self-adaptive geometric module and a physical field numerical simulator are difficult to fuse, and the dynamic geometric data format conversion efficiency is low are solved.