The wake effect is one of the leading causes of energy losses in offshore wind farms (WFs). Both turbine placement and cooperative control can influence the wake interactions inside the WF and thus the overall WF power production. Traditionally, greedy control strategy is assumed in the layout design phase. To exploit the potential synergy between the WF layout and control so that a system-level optimal layout can be obtained with the greatest energy yields, the layout optimization should be performed with cooperative control considerations. For this purpose, a novel two-stage WF layout optimization model is developed in this paper. Cooperative WF control of both turbine yaw and axis-induction are considered in the WF layout design. However, the integration of WF control makes the layout optimization much more complicated and results in a large-scale nonconvex problem, hindering the application of current layout optimization methods. To increase the computational efficiency, we leverage the hierarchy and decomposability of the joint optimization problem and design a decomposition-based hybrid method (DBHM). Instead of manipulating all the variables simultaneously, the joint optimization problem is decomposed into several subproblems and their coordination. Case studies are carried out on different WFs. It is shown that WF layouts with higher energy yields can be obtained by the proposed joint optimization compared to traditional separate layout optimization. Moreover, the computational advantages of the proposed DBHM on the considered joint layout optimization problem are also demonstrated.