More accurate navigation systems are always required for autonomous unmanned underwater vehicles (AUUV)s under various circumstances. In this paper, a measuring complex of a heavy unmanned underwater vehicle (UUV) was investigated. The measuring complex consists of an inertial navigation platform system, a Doppler lag (DL) and an estimation algorithm. During a relatively long-term voyage of an UUV without surfacing and correction from buoys and stationary stations, errors of the measuring complex will increase over time. The increase in errors is caused by an increase in the deviation angles of the gyro platform relative to the accompanying trihedron of the selected coordinate system. To reduce these angles, correction is used in the structure of the inertial navigation system (INS) using a linear regulator. To increase accuracy, it is proposed to take into account the nonlinear features of INS errors; an adaptive nonlinear Kalman filter and a nonlinear controller were used in the correction scheme. Considering that, a modified nonlinear Kalman filter and a regulator in the measuring complex are proposed to improve the accuracy of the measurement information, and modification of the nonlinear Kalman filter was performed through a genetic algorithm, in which the regulator was developed by the State Dependent Coefficient (SDC) method of the formulated model. Modeling combined with a semi-natural experiment with a real inertial navigation system for the UUV demonstrated the efficiency and effectiveness of the proposed algorithms. Doppler lag, which are combined into a measuring complex (MC). The INS and lag signals are processed together using the Kalman filter [8][9][10][11].When the UUV is working under ice fields in the Arctic, there is no possibility of periodic ascent to the surface of the sea; thus, INS correction from a gyro-stabilized platform (GSP) is not provided. In the case of long-term autonomous navigation with the use of a strapdown INS, errors increase over time due to the instability of sensitive elements. Moreover, when UUVs perform maneuvers to complete tasks with long-term autonomous navigation, even for platform INS, errors will reach large values. This is due to an increase in the deviation angles of the gyro-stabilized platform (GSP) relative to the accompanying coordinate system (SC). Even with the correction of INS from a lag and information processing by the Kalman filter, errors of the navigation information increase as the model of INS errors in the Kalman filter becomes inadequate for the real process.Considering the prospective applications, scientists have been interested in AUUVs and all the particular constraints in different media have been formulated into mathematical problems. Wu et al.[12] generated the optimal paths based on the Particle Swarm Optimization (PSO) algorithm and the Kalman filter to finish an underwater target strike mission; Batista et al. [13] proposed a filtering method with applications to estimate the linear motion of underwater vehicles, taking into considert...