Agitation error caused by ocean wave is the key factor affects the real time rapidity and accuracy of the initial alignment for ship. Considering the characteristic of strap down inertial navigation system (SINS) for the ship is on mooning, a fast mooring initial alignment based on inertial frame for measurement vehicle was proposed in this paper. The initial strap down matrix was calculated indirectly by making use of the components of gravity in different coordinate frame, and the inertial coarse alignment of INS was set. Mooring experiment results showed that, the inertial frame alignment method which was proposed in this paper could improve the real time rapidity and alignment accuracy, and satisfy the requirement of real time and high accuracy of the initial alignment for ship.