Defining the spatial arrangement and length of the cutting cycle in a logged area is crucial for reconciling potential conflicts between timber yields and maintenance of ecosystem services in natural forests. In this study, we investigated long-term impacts of clear-fell logging on timber production and tree species diversity in a subtropical forest on the Ryukyu Islands, using an individual-based simulation model. We assumed six logging scenarios defined by combinations of forest type and regeneration processes, which acted as surrogates for spatial scales of clear-fell logging. These scenarios were simulated under cutting cycles ranging from 20 to 150 years. Short-cutting cycles resulted in dominance by the sprouting species Castanopsis sieboldii. The compositional shift was accelerated by the lack of seed dispersal from surrounding forest areas. The simulations demonstrated that a sustainable logging regime maintaining both yield and tree species diversity requires a cutting cycle longer than 50 years. The simulation results also suggest that the trade-off between the recovery of tree species diversity and timber production is favored more in stands surrounded by mature forest than in isolated stands or stands surrounded by immature forest. Ecological risk assessments based on model simulations provide an alternative to current forest management practices that rely on empirical knowledge.