The effect of seasonality is one of the most significant external sources of variation affecting cambial activity and the development of newly divided cells, and therefore influencing stem growth of trees. Here, we investigated changes in the seasonal concentrations of metabolites of current-year stem tissues in 6-year-old Pinus densiflora at June, August, and October. 76, 75, and 78 metabolites were assigned at June, August, and October by GC/MS. Among these compounds, 55 metabolites were commonly found in all three times, and they were divided into six groups according to the variation of concentrations in each times. Among 56 metabolites, the concentrations of three inositol-methylated derivatives, myo-inositol, ononitol, and pinitol in current-year stem tissues at August were significantly correlated with the heights of nursery-grown trees. Furthermore, we found that such metabolites were significantly correlated with stem diameter at 27 years for two consecutive years. Therefore we suggest that seasonal differences in the contents of inositol derivatives may explain much of the natural variation seen for tree stem size in even-aged pine forests. And these have the potential as metabolic markers of inherently rapidly growing trees in the early selection of those conifer families.