A Laser Scanning aided Inertial Navigation System (LSINS) is able to provide highly accurate position and attitude information by aggregating laser scanning and inertial measurements under the assumption that the rigid transformation between sensors is known. However, a LSINS is inevitably subject to biased estimation and filtering divergence errors due to inconsistent state estimations between the inertial measurement unit and the laser scanner. To bridge this gap, this paper presents a novel integration algorithm for LSINS to reduce the inconsistences between different sensors. In this new integration algorithm, the Radial Basis Function Neural Networks (RBFNN) and Singular Value Decomposition Unscented Kalman Filter (SVDUKF) are used together to avoid inconsistent state estimations. Optimal error estimation in the LSINS integration process is achieved to reduce the biased estimation and filtering divergence errors through the error state and measurement error model built by the proposed method. Experimental tests were conducted to evaluate the navigation performance of the proposed method in Global Navigation Satellite System (GNSS)-denied environments. The navigation results demonstrate that the relationship between the laser scanner coordinates and the inertial sensor coordinates can be established to reduce sensor measurement inconsistencies, and LSINS position accuracy can be improved by 23·6% using the proposed integration method compared with the popular Extended Kalman Filter (EKF) algorithm.