The invention discloses a robot active force compliance pinhole butt joint assembly method based on a Hertz elasticity model. According to the method, automatic butt joint of robot active force compliance pinholes is conducted according to a force compliance control manner, and under the guidance of a guide pinhole, a robot makes the mounting face of mounted equipment or a deck attached to the mounted face. The improved force compliance control manner is characterized in that control is conducted by additionally arranging an elastic contact mathematical model and a friction model based on an impedance force compliance control manner. According to the robot active force compliance pinhole butt joint assembly method, by additionally arranging the mathematical model, force sensor informationand robot tail end posture information are corrected, the system feedback quantity fed back to a controller is more precise, and the force compliance mounting problem of large instrument equipment anddecks in spacecraft assembly is solved, and the assembly quality and assembly efficiency are improved.