For marine engine, the quality of the crankshaft is a decisive factor for its mechanical life. In the manufacturing processes of semi-built-up marine crankshaft, as the final process, finish machining of the entirety is vital for the crankshaft quality. Applying finite element method, the traditional way for clamping was analyzed and the problem of machining deformation because of poor rigid was pointed out. In addition, a new clamping method was put forward according to the structure characters of crankshaft, which provided technical support for theory research and practical manufacturing. Moreover, a further research direction to increase the machining quality was proposed.