CAVs (Connected Autonomous Vehicles) can be effective in improving the efficiency of transportation, but heterogeneous multi-modal traffic flows may hinder this efficiency. This paper addresses the issue of heterogeneous traffic flows affecting the efficiency of transportation when CAVs enter the market, and proposes a joint dedicated lane for CAVs and buses. In the bi-level program model for the joint dedicated lane, the lower-level is aimed at the multi-modal traffic assignment problem, while the upper-level is aimed at system optimality. For the lower-level, the paper examines the characteristics of various traffic flows in a mixed traffic flow, investigates the impact of CAV mixing on the road link’s capacity, calculates the travel time of various traffic modes accordingly, and generates a generalized travel cost function for each mode, which is solved using the diagonalized weighted successive averaging method (MSWA) algorithm. The upper-level issue considers the continuity of dedicated and non-dedicated road segments, and the goal is to reduce the overall cost for all travelers by utilizing the dedicated road deployment scheme as the decision variable, which is addressed using a genetic algorithm. Finally, numerical examples and sensitivity analyses are designed accordingly. The numerical example demonstrates that the joint dedicated lane not only lowers the overall cost of the system, but also enhances the efficiency of CAV and bus travel, optimizing the road network and promoting bus and CAV travel modes. The sensitivity analysis shows that in order to set up a joint dedicated lane, the frequency of bus departures and the penetration of CAVs are conditions that must be considered, and that the benefits of a joint dedicated lane can only be fully realized if the frequency of bus departures and the penetration of CAVs are appropriate.