Preferential flow is considered to play an important role in the conduction of soil water. However, during a natural rain event, whether this significance changes or not and how it changes are still not understood. In this paper, by analyzing three-dimensional spatial and temporal variations of soil water content at two field sites, temporal variations of the three-dimensional rainfall infiltration process in a heterogeneous soil were studied. The three-dimensional soil water contents were obtained by soil moisture tomography. For eight selected rain events, temporal variations of infiltration area, homogeneity of the infiltration process, and average water content increment were analyzed. Relationships between the infiltration homogeneity and the infiltration area and the average water content increment were investigated. The results show that the three-dimensional rainfall infiltration in heterogeneous soil varies with rainfall process. For rain events with short duration time and low rain intensity, the infiltration process behaves preferentially and heterogeneously. The preferential flow plays an important role in the conduction of soil water. For rain events with long duration time and high rain intensity, the infiltration process shows more homogeneous and plug-like characteristics. The preferential flow becomes less important. In a rain event, during the initial period of the rain, the infiltration process usually is heterogeneous and preferential, starting from partial areas in the layers. However, with continuing rainfall, the infiltration area gradually expands to the entire layers and the infiltration process becomes more homogeneous and plug-like.