In recent years, many cities have experienced serious urban flood and non-point pollution issues due to hydrological process changes in rapidly urbanizing areas. Understanding the relationship between impervious surface and direct runoff is important for urban planning to protect the urban hydrological system. In this study, we used a mixed spectral decomposition method to interpret the long-term series of impervious surface of Shenyang, China. Direct runoff was evaluated by an improved SCS-CN model, and the relative influences of five underlying surface factors on the direct runoff of each period were analyzed by boosted regression trees. The overall impervious area was significantly increased in both the study area and built-up area from 1984 to 2015. The impervious ratio showed a decreasing trend in the built-up area and increasing trend in the whole study area. The runoff coefficient of the built-up area showed a significantly decreasing trend. The runoff ratio of the built-up area to the whole study area was increased dramatically, reaching 0.26 by 2015. NDVI, vegetation, and impervious surface were the most important urban surface conditions in the study area for direct runoff generation. The relative influence of impervious surface showed a rapidly increasing trend and then gradually decreased from 2000.