To understand the responses of terrestrial vegetation in central Japan to global climate changes, we generated a record of lignin composition from core BIW08-B in Lake Biwa, central Japan, during the last 147,000 years by TMAH–pyrolysis–GC/MS. Lignin abundance was intermittently elevated and associated with a high ratio of cinnamyl (C) to vanillyl (V) phenols (C/V ratio) of lignin, suggesting episodic inflows of herbaceous plant-derived organic matter into Lake Biwa. The largest inflow occurred during the last deglaciation. Variation in the ratio of syringyl (S) to vanillyl (V) phenols (S/V ratio), which is a contribution index of angiosperms against gymnosperms, showed a precession-like cycle, was consistent with a pollen record from Lake Biwa, and showed a pattern similar to the S/V record from an offshore marine site in the northwestern Pacific. The variation reflected the regional replacement of cool-temperate deciduous broadleaf forests, subalpine conifer forests, and Japanese cedar forests in central Japan caused by the repetition of warmer, dry and cooler, wet climates on a precession cycle.