Urbanization can not only change the landscape types and composition, but also change the spatial morphology and decrease the natural habitat connectivity. Depicting the spatial relationship between artificial surface, arable land and natural habitat is of great significance to examine the landscape ecological effects, especially for the interaction between different landscapes and changes of structure and function. The effects of fragmentation and morphological changes on landscape connectivity with urban expansion of Kunming City, Yunnan Province in 1990-2015 were analyzed in this study by using the urban fragmentation index (UFI) to depict the level of landscape fragmentation. Based on morphological spatial pattern analysis (MSPA), seven landscape morphological elements (core, islet, bridge, loop, perforation, edge, and branch) of arable land and natural habitat were obtained. Three edge widths were selected to compare the influence of edge widths on the landscape morphology. The landscape connectivity changes were evaluated by probability of connectivity (PC) and importance value of patches (dPC). The average UFI and dPC were calculated on the grid of 4 km×4 km, and the correlation among different variables were analyzed by the three-dimensional curved surface graph. The results showed that the artificial surface in Kunming has been expanding, occupying a large amount of arable land. The annual increase rate of landscape fragmentation has been increasing in the past 25 years. The results of MSPA indicated that the arable land showed a continuous and stable declining trend, and the landscape morphology of natural habitat showed little change from 1990 to 2010. After 2010, there has been a dynamic process from stability to fluctuation and then to fragmentation. There were significant differences between different edge widths. The wider the edge width was, the more obvious the change of connectivity was. This fact indicated that urbanization had a more serious impact on small green patches. The change of dPC was consistent with that of the UFI, and the change was concentrated in the eastern region of Kunming. With the increase of the UFI, the landscape connectivity decreased year by year. The correlation analysis showed that the landscape connectivity experienced a process from fluctuation to steady decline with the increase of fragmentation. In general, the urbanization of Kunming has caused continuous reduction of arable land. Although the loss of large-scale natural habitat has not been caused by the urbanization, the connectivity has been reduced to a certain extent. It is necessary to control the spatial pattern to avoid the negative impact of the urbanization on the overall landscape connectivity.