Contraflow left-turn lane (CLL) design has been increasingly applied in China to relieve traffic congestion at signalised intersections. Existing studies evaluate the impacts of the CLL design, optimise the length of the contraflow left-turn lane, and propose actuated signal control strategies with a fixed signal phase sequence. We set up constraints to ensure the safety of the generated signal timing plan, employ the cell transmission model (CTM) to capture urban traffic dynamics, and formulate the optimisation of the CLL design at intersections as a Mixed-Integer Linear Programming (MILP) model. Our model optimises the length of the contraflow lane, signal phase sequence, and green time duration considering traffic dynamics and spatial holding capacities of links. Numerical experiments are conducted with real traffic volume data collected in Shenzhen, China, which show that our approach reduces the delay by 9.63% and increases the capacity by 11.48% compared with the actuated CLL design.