Urbanization with mismanagement has seriously threatened regional ecology and cultivated land security. At present, the territorial spatial usage regulations often isolate functions from a single aspect, which makes it difficult to meet demands of regional economic development, ecological protection, and sustainable development. This paper attempted to construct a zoning system of territorial spatial usages that comprehensively considers local development demands, resource endowment conditions, and sustainable development, and proposed a method to regulate sustainable development intensity. Wuhan City was selected as the study area. At first, the land resource function was zoned by the modified multi-objective land allocation (MOLA) model considering the resource endowment conditions and social development demands. The study area was divided into ecological, agricultural, and construction land resources. Also, the functions of land, water, and geological resources are integrated into the zonation framework of territorial spatial usages. Then, the construction and agricultural development intensity in different usage areas were quantitatively regulated by comprehensively considering the current basic demands, sustainable development, land use status, and relevant policies. The calculation results show that the development intensity of construction land in the construction space should be limited to 43%–53%, while the development intensity in the general farmland area should be limited to 10%. The agricultural development intensity should be greater than 65% in the general farmland, while it should be lower than 64% in the general ecological function area. Additionally, by comparing with the land-use status, the construction in the study area is within a reasonable scope (about 44%). The north and south of Huangpi District, the north of Xinzhou District, Hannan District, and the east of Caidian District still have great potential for development. Finally, based on territorial spatial usage and development intensity regulation, this paper proposed some effective suggestions for territorial spatial development. This paper can provide a reference for the territorial spatial planning and ecological environment protection of Wuhan City. At the same time, it provides a new idea for urban planning research considering the resource, environment, and economic development.