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Prostrate stems represent an important morphological component of Fagus crenata (Siebold’s beech). This unique stem-bending growth strategy has led to the dominance of this tree species in regions with heavy snowfall along the Sea of Japan. We investigated the early-stage aboveground–belowground dynamics of F. crenata by applying allometric scaling theory to analyze morphological development in saplings (aged 3–20 years). Samples were collected from 25 trees in three forests in Nagano, central Japan. The scaling exponent ( b ) demonstrated an increase in the fraction of aboveground biomass (i.e., dry mass) in relation to the overall surface area (aboveground, b = 0.748; belowground, b = 0.626) and biomass (aboveground, b = 1.087; belowground, b = 0.983). These values are highly consistent with recent field observations by other researchers. Aboveground biomass growth was supported by the increasing role of prostrate stems in belowground development ( b = 1.114). Despite its extension belowground, the growth properties of the prostrate stem may be identical to those of shoots, as both are directly influenced by nutrient sources above the germination point. Our findings highlight the significance of the prostrate stem in supporting beech survival in areas with heavy snowfall.