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Ultrashort baseline positioning systems are used to localize manned deep-sea submersibles. A long baseline positioning system is a significant supplement to an ultrashort baseline positioning system and provides more precise positioning. The long baseline beacon array design applied is a primary factor affecting the accuracy of long baseline positioning. However, beacon array designs have mainly been studied in autonomous underwater vehicles (AUVs). Because the characteristics and dive tasks between AUVs and manned deep-sea submersibles are different, the simple beacon array formations used in AUVs cannot be directly used in manned deep-sea submersibles. To the best of our knowledge, this study is the first to present the optimal design of a beacon array for a long baseline positioning system used in manned deep-sea submersibles. In this paper, based on the characteristics of a manned deep-sea submersible, the seven basic principles used for the optimal design of a long baseline beacon array are presented. First, the dive tasks of a JIAOLONG manned deep-sea submersible are analyzed, including the relationship between the dive survey lines, and the depth and distance of each line. Second, we explore the minimum beacon number to cover the dive site and its vicinity. Third, we adjust the beacon position based on the seven optimal design principles. The beacon array is designed to satisfy manned deep-sea submersible dive requirements during the JIAOLONG Test Applications Voyage 2013. A sea trial demonstrates that the long baseline positioning results are reliable if at least three beacons are not blocked, and the accuracy of the long baseline positioning system is better than that of an ultrashort baseline.