The control allocation algorithm is developed for a class of distributed control systems with hierarchical structure and similar models of the subsystems, to solve the real-time cooperative control taking the dynamics and possible variations of subsystems into consideration. The augmented state-space model of the subsystems is first established for the control allocation. Based on robust control theory, the constrained and convex optimization is then developed with LMIs form to design the gain matrix of the dynamic control allocation. Furthermore, the closed-loop stability of the distributed control system is analyzed on the basis of stable upper-level main control law. Finally, simulations on the four-corner leveling control system of an advanced hydraulic press demonstrate the effectiveness of the proposed control allocation algorithm.