Identifying effective management operations for plantations is important for conservation of biodiversity in a plantation-dominated landscape. We tested whether pre-commercial thinning influenced community structures and could be an effective strategy for increasing diversity and abundance of plants and animals in plantations. We designated thinned and unthinned study stands in Japanese cedar (Cryptomeria japonica) plantations and compared the communities of understory vegetation, bees, butterflies, hoverflies, and longhorn beetles 1 and 3 years after thinning. The analyses of vegetation showed that pre-commercial thinning affected community structure, but species richness and vegetation abundance were not significantly affected. Thinning affected insect community structure, and both species richness and abundance of all insect groups increased 1 year after thinning. However, 3 years after thinning, significant differences only remained in the species richness of bees and the abundance of bees, butterflies, and hoverflies. These results suggest that pre-commercial thinning in plantation stands influences the community structure of understory vegetation and can be an effective way to increase the diversity and abundance of some insect groups in the short term. However, the results also suggest that the duration of the operational effects of pre-commercial thinning varies among insect groups; thus, the variable effects of pre-commercial thinning should be carefully considered in the conservation-based management of plantation stands.