With advanced connected automated vehicles (CAVs) technologies, joint optimisation of trajectories and signal control can significantly improve traffic mobility and safety. This study presents a joint optimisation method of trajectory and signal control at intersections mixed with human-driven vehicles (HVs) and CAVs based on vehicle departure sequence estimation. First, a signal control optimisation method based on the trajectories detected by CAVs was proposed. By estimating the virtual arrival time of HVs and CAVs, the optimal departure sequence with minimal delay was determined. Then, a joint optimisation of trajectories and signal control was developed depending on the position of CAVs in the mixed vehicles platoon, i.e. leader and follower. Simulation experiments under different scenarios were conducted to analyse the performance of the proposed method. Comparison results show that the method decreases the average delay by 19.66% when the CAV’s penetration rate ranges from 10% to 20%.