Throughfall (TF)—as a diffusive hydrological water flux—significantly affects ecohydrological and biogeochemical processes within forest ecosystems. Recent investigations have revealed the impact on TF generation processes within unmanaged coniferous plantations of under-canopy structures, particularly those laden with dead branches, as well as upper-canopy structures. However, spatiotemporal variations in TF in such plantations remain unexplored. We investigated these variations in TF in a 33-year-old unmanaged Japanese cypress (Chamaecyparis obtusa Endl.) plantation, laden with dead branches, with a high stand density (SD) of 2,500 stems ha−1. Over a two-year period (May 2017 to May 2019), we conducted weekly TF measurements using 28 manual-type TF collectors. We compared the present TF ratio and canopy water storage capacity (S) with those of previous investigations conducted on Japanese cypress plantations. Moreover, we assessed key indices contributing to spatiotemporal TF variations (canopy cover: CC and distance to the nearest stem: TFd) and potentially influential dead branch indices (number of dead branches: TFdb and vertical spacing length on a stem: TFs) to elucidate TF spatial patterns. The results showed that the TF ratio was notably lower than that in previous studies (n = 13), with SD (r = –0.92, p < 0.001) and S (r = –0.87, p < 0.001) emerging as key influential factors among other stand-structure parameters. Spatial TF patterns exhibited a decreasing trend as the gross rainfall (GR) increased. Temporal stability was not significantly associated with CC (r = 0.120, p = 0.544), TFd (r = 0.068, p = 0.731), TFdb (r = 0.211, p = 0.281), or TFs (r = 0.206, p = 0.292) for any of the TF collectors. These findings underscore the important role of GR in determining the spatial variation of TF. Collectively, our results contribute to an enhanced understanding of TF spatiotemporal heterogeneity in unmanaged Japanese cypress plantations with dead branches.