The seedling stage is critical in the life cycle of trees, and performance is controlled by both abiotic and biotic factors, which are spatially heterogeneous. We investigated the relationships between the seedling survival or growth of Fagus crenata and seven potentially influencing factors (culm density of dwarf bamboo, slope angle, topographic convexity, distance from the nearest conspecific adult, and local density of F. crenata seedlings, and seedling size and age), under consideration of the changes in direction and strength of the microtopographic effects across space. In 2011, we identified all F. crenata seedlings (maximum stem length <50cm) within a 90x30-m plot in a cool-temperate forest in western Japan and then recorded their survival and growth of stem length in 2012. The best model based on Akaike's information criterion indicated that the size, age, and distance had positive effects on the survival while slope and convexity had negative effects, and that the strength of the negative effect of convexity varied spatially even within our plot. Meanwhile, the size and culm density had positive and negative effects on the growth, respectively. These results suggest that F. crenata seedlings have more chance to survive at the site on a gentle slope with planar or relatively concave undulations, where the conspecific adults stood apart, and that the seedlings show higher growth rate at the sites without dense dwarf bamboo. Furthermore, we demonstrate that the spatially nonstationary effect of microtopography controls the spatial pattern of seedling survival.