The array position and orientation system (array POS), composed of one main POS and multiple sub-inertial measurement units (sub-IMUs), is key equipment in the aerial remote-sensing system, especially the multi-load system, which can provide motion compensation for the multi-load remote-sensing system to improve imaging quality. Nevertheless, the measurement information of each sub-IMU can only realize the motion information of the corresponding remote-sensing load. Ideally, each remote-sensing load should be equipped with a sub-IMU for motion compensation, which is impossible in actual engineering considering the volume, weight and cost. To solve this problem, a multi-node motion estimation method based on the B-spline of the array POS is proposed to realize the motion compensation of remote-sensing loads without sub-IMUs. Firstly, the transfer alignment method based on fiber-grating multi-dimensional deformation measurement was adopted. Motion parameters of the remote-sensing payload equipped with sub-IMUs at different times can be obtained by observing and correcting the errors between the main POS and sub-IMUs. In this way, the space-time characteristics of each interpolation point are fully utilized. Additionally, the motion information of the main POS and all sub-IMUs is fitted through the estimation method based on the B-spline, during which wing deformation is considered to obtain the motion parameters of the remote-sensing payload equipped without a sub-IMU. In this way, the spatial correlation between the information of each node is fully utilized. Due to the full utilization of the spatiotemporal correlation of the motion information of each sub node, high-precision and highly reliable motion information of the remote-sensing loads not equipped with sub-IMUs is obtained. Furthermore, the proposed method can be modified locally without affecting other nodes, and has the advantages of a simple algorithm and easy engineering implementation. Finally, a semi-physical simulation based on ground-loading test was conducted. The results show that the baseline in the X-axis, Y-axis and Z-axis direction is improved by 0.484 mm, 0.137 mm and 1.225 mm, respectively, and that the measurement accuracy of roll angle is improved by 0.011°.