Mixed Vehicle-bicycle flow is a typical feature of urban traffic. Vehicles are frequently interfered by Bicycles will lead to increased delays in vehicle travel, reduced Vehicle speed of traffic flow, and decreased the accumulation of vehicles on local roads. In this paper, a theoretical analysis method of 3D-Macroscopic Fundamental Diagram is proposed to explore the microscopic operation characteristics and macroscopic evolution law of mixed traffic flow. Firstly, a cellular automaton model describing the bicycle traffic flow and a cellular transmission model describing the vehicle traffic flow are established respectively. Then, the Simulink simulation platform was built and the coupled model was run to obtain the 3D-Macroscopic Fundamental Diagram of the road network. Finally, two methods were designed to improve the proportion of isolation in the road network and to increase the width of bicycle lanes The results show that the 3D-Macroscopic Fundamental Diagram can quantify the impact of conflict, guide the governance of mixed traffic congestion, and provide technical support for improving the travel order and environment of urban traffic.