Abstract In order to solve the contradiction between incomplete thresh, separation loss, and grain breakage rate during the harvest of super hybrid rice by the conventional threshing and separating unit for the head‐feed combine harvester, the segmented‐differential threshing and separating unit for the head‐feed combine harvester was developed. The unit was mainly composed of a coaxial segmented‐differential threshing drum and rotary concave screen. This paper expounds on the structure and working principle of segmented‐differential threshing and separating unit. With the rotate speed of the segmented‐differential drum, the linear velocity of the rotary concave screen, and the clamping chain speed as the test factors, the grain loss rate, breakage rate, and impurity rate as the performance indicators, three‐factor quadratic regression orthogonal rotation combination design test is performed. This paper analyzes the test results by using the Design‐Expert6.0.10 software, establishes a performance indicator mathematic model of the threshing and separating unit, and determines the optimal working parameter combination. Moreover, this paper performs a contrast test of the segmented‐differential threshing and separating unit to the conventional single‐speed unit, and using MATLAB software to establish a distribution model of threshed materials and make an analysis. Results show that when the rotate speed of low‐speed/high‐speed drum in the segmented‐differential threshing and separating unit was 505/680 r/min, the linear velocity of the rotary concave screen was 1 m/s and the clamping chain speed was 1.26 m/s, the grain loss rate, breakage rate, and impurity rate were 1.94%, 0.21%, and 0.56%, respectively.