The oceans are three-dimensional (3D) spaces, resource redistribution has long tended to involve two-dimensional (2D) planning, which has obscured the resource attributes and ecological features of the ocean's different layers, and is prone to cause erroneous sea-use conflicts. This study established a new 3D marine spatial planning (MSP) method consisting of ecological protection zoning (EPZ) and intensive sea-use zoning (ISZ) programs involving marine 3D spatial laying: EPZ was determined using a Marxan model. Based on spatial idleness and environmental friendliness principles, and appropriate newly added sea-use activities were designed to form synergistic sea-use combinations to establish an ISZ program. A case study of Qidong was conducted to test the applicability of the 3D planning program and compare the differences in the zoning results according to the two scenarios of ecological protection and exploitation. Results indicated that EPZ of mid-bottom waterbodies accounted for the highest proportion (47.62%). The best solutions and planning units selected frequency grading could be achieved separately for two scenarios of EPZ. For ISZ, the zoning for both scenarios achieves a synergistic effect between the newly added sea-use activities in the transportation zone; through the northward shift of sea-use in the southern fairway of Qidong, this sea-use activity converted the initially antagonistic attributes with the ecological protection zone to a synergistic purpose. Differences in the results of the intensive sea use zoning between the two scenarios were manifested in the EPZ and surrounding sea use activities, focusing on fishing and ecological control zones and the arrangement of wind power. The 3D MSP methods can address the conflict between some sea-use activities in 2D planning and the conflict between stakeholders competing for the sea-use right, and it also provides a solution for the coastal government to redistribute the marine resources and coordinate the sea-use elements. The relevant practice can provide theoretical and technical support for ecological protection, intensive and economical utilization of marine spatial resources, and national spatial planning framework improvement.