Under the background of New-type Urbanization, with the continuous advancement of urbanization and the all-round development of cities, all kinds of demands are also rising. In the case of demand, it is difficult to quickly adjust from the land supply side and to guide the optimization of the structure and layout of land use is one of the methods to achieve this based on the current situation and shortage of urban land use structure and spatial arrangement. Because of the complexity, uncertainty and dynamics of the land use system, it is necessary to use an uncertain model to accurately describe and propose the approximate optimal solution, so this study analyzes the influencing mechanism of land use and optimize the land use structure under uncertainties by using a Bayesian network and fuzzy mathematical programming. Based on the results of the two stages of analysis, the cellular automata simulation is completed. The framework is applied to Chongzhou city in western China. The results indicated that the optimal land space for cultivated land is in the middle and the south based on the joint influence probability of arable land and urban construction land. The conversion probability of the area near the east is low, and the joint impact probability of construction land in all areas is generally similar except for the western protection area. After the optimization of the fuzzy planning, the optimal construction land scale is 69.42 km2. Under the condition that the cultivated land’s red line is guaranteed, there is still 98.87 km2 of space for the increase in cultivated land. It is found through simulation that the increase in construction land would occur in the central and western parts of Chongzhou, which may be caused by the urban siphon effect. According to Monte Carlo verification, when the conversion probability exceeds 50%, the cultivated land could be turned into urban construction land, with an accuracy of 91.99%. Therefore, this proposed framework is helpful to understand the process of land use and provides a reference for making scientific and reasonable territorial spatial planning and guiding land use practice under uncertainties.