Abstract: This paper introduces and realizes a topological simplification of 3D scalar fields with physical feature preservation to solve the physical feature loss problem by pre-existing methods.This paper classifies the scalar field region under the application-specified physical criterion，and combines the feature detection of a vector field with its topological simplification.By constructing Morse-Smale complex over the physically less important subregions and proceeding by repeatedly removing a pair of critical points from the complex，the topological feature is simplified and smoothed，this method is based on the morse theory.The experimentation verifies the feasibility of the method.