For acceleration control missile，flat output is difficult to find，moreover，nonminimum phase problem is hard to cope with. A new sliding mode control method was introduced to deal with nonminimum phase problem in acceleration control of anti-vessel slide-to-turn missiles，from which flat output was constructed and the unstable system matrix was stabilized. Real-time trajectory generation algorithm based on flatness was given. With the help of flatness character，windup phenomena which often brought out by missile control system constraints tends to happen less. Simulation was made for verification of the algorithm.