Much attention is now being paid to secondary woodlands because of their high biodiversity. Especially in hilly areas, variations in both micro-scale landform and vegetation management are important factors in maintaining plant species diversity. Our objective was to clarify the influence of the two factors on the species composition of the herbaceous layer of Quercus serrata secondary woodlands and their verges to paddy fields in the western Tama Hills, central Japan. Seven transects were set on hillslopes that had typical arrangements of micro-scale landform units, and 159 quadrats measuring 2 m × 2 m were set along them. Plant species that appeared in the herbaceous layer were recorded, and the relative light intensity and soil moisture were measured in each quadrat. Ordination by Detrended Correspondence Analysis showed that two environmental factors had significant effects in determining the species composition: light condition, which was influenced mainly by vegetation management, and soil moisture, which varied along the arrangement of micro-scale landforms from crest slopes to lower side slopes and head hollows. We found that micro-scale landform affected vegetation structure. The effect is more complicated on the lowermost slopes adjacent to paddy fields in the valley bottoms, because these slopes are disturbed by the unstable land conditions and intensive management.