Distributed inertial sensor network possesses low cost, high fault tolerance and high reliability. Based on the configuration of the sensor network structure, the relationship between the main and child nodes' inertial outputs is analyzed in the distributed inertial sensor network. The new method of transfer alignment is researched by distributed inertial network technology. On the condition that the carrier structure has serious deformation, the carrier deformation estimation can improve the alignment accuracy of the sub-navigation system. Therefore, the inertial measurement matching algorithm modified by Three-Axis Attitude Determination (TRIAD) algorithm is proposed to estimate carrier deformation angle. The simulation results show that the precision of the inertial information in the sub-navigation system is improved by estimating carrier deformation angle to transfer alignment.