Subsurface flow is a prominent runoff process in sloping lands of purple soil in the upper Yangtze River basin. However, it remains difficult to identify and quantify. In this study, in situ runoff experimental plots were used to measure soil moisture dynamics using an array of time domain reflectometry (TDR) together with overland flow and subsurface flow using isolated collecting troughs. Frequency of preferential flow during rainfall events and the controls of subsurface flow processes were investigated through combined analysis of soil properties, topography, rainfall intensity, initial wetness, and tillage. Results showed that subsurface flow was ubiquitous in purple soil profiles due to well-developed macropores, especially in surface soils while frequency of preferential flow occurrence was very low (only 2 cases in plot C) during all 22 rainfall events. Dry antecedent moisture conditions promoted the occurrence of preferential flow. However, consecutive real-time monitoring of soil moisture at different depths and various slope positions implied the possible occurrence of multiple subsurface lateral flows during intensive storms. Rainfall intensity, tillage operation, and soil properties were recognized as main controls of subsurface flow in the study area, which allows the optimization of management practices for alleviating adverse environmental effects of subsurface flow in the region.