Aiming at the problems of low accuracy and high complexity of localization algorithm in three-dimensional space, a Non-Full Sequence-based Localization (NFSL) algorithm for 3D underwater sensor networks was proposed. Different from traditional sequence-based localization algorithms, a more realistic situation where communication range of beacon nodes is not entire network was taken into consideration by NFSL. Firstly, 3D Voronoi diagram was used to divide the 3D location space and thus virtual beacon nodes as well as their rank sequences were determined. Secondly, the nearest beacon node was obtained according to the rank correlation coefficient between the unknown node sequence based on Received Signal Strength Indication (RSSI) and the beacon node sequence, and the nearest sequence table was constructed. Next, an algorithm which aimed at the similarity of sequences with unequal lengths was designed and utilized to obtain the rank correlation coefficients between the non-full sequence of unknown nodes and each sequence in the nearest sequence table. Finally, the weighted estimation of the unknown node's location was realized by taking the rank correlation coefficient as the weight. In simulation experiments, the localization accuracy of NFSL was compared with that of DV-Hop and Centroid by taking the ratio of beacon nodes, communication range, total number of nodes and network scale as variables. The extensive simulation results verified the effectiveness of the proposed algorithm. Besides, its localization accuracy significantly improves with the increasing number of beacon nodes. Compared with traditional localization algorithms, the localization accuracy of NFSL is improved by as much as 23%.