China’s rapid urbanization and industrialization process has triggered serious air pollution. As a main air pollutant, PM2.5 is affected not only by meteorological conditions, but also by land use in urban area. The impacts of urban landscape on PM2.5 become more complicated from a three-dimensional (3D) and land function zone point of view. Taking the urban area of Nanchang city, China, as a case and, on the basis of the identification of urban land function zones, this study firstly constructed a three-dimensional landscape index system to express the characteristics of 3D landscape pattern. Then, the land-use regression (LUR) model was applied to simulate PM2.5 distribution with high precision, and a geographically weighted regression model was established. The results are as follows: (1) the constructed 3D landscape indices could reflect the 3D characteristics of urban landscape, and the overall 3D landscape indices of different urban land function zones were significantly different; (2) the effects of 3D landscape spatial pattern on PM2.5 varied significantly with land function zone type; (3) the effects of 3D characteristics of landscapes on PM2.5 in different land function zones are expressed in different ways and exhibit a significant spatial heterogeneity. This study provides a new idea for reducing air pollution by optimizing the urban landscape pattern.