High-resolution and high-precision marine gravity reference maps are core prerequisites for the practical application of gravity-assisted inertial navigation algorithms, and their accuracy directly determines the performance of the navigation system. In view of the problems existing in the current geographic rectangular grid gravity reference map, such as severe polar deformation, poor adjacent consistency, and low positioning accuracy in high latitudes, this study introduces a hexagonal grid system to construct a gravity reference map. It systematically analyzes its compatibility and accuracy in navigation applications. A multi-resolution hexagonal grid scheme with a 7-aperture structure is further proposed to meet the characterization requirements of gravitational fields with different complexities. Experimental verification shows that the accuracy of the gravity-assisted inertial navigation algorithm improved by 0.4%, while that of gravity sequence matching improved by 50%. The proposed hybrid resolution grid can achieve a maximum gravity data compression rate of 68% while ensuring navigation accuracy, especially with regard to the computational efficiency and accuracy requirements of gravity-assisted inertial navigation.