Abstract: This study aims to explore the “seed-seedling transition paradox” in the mesophytic Picea schrenkiana var. tianschanica forest. Monitoring quadrats were established to observe spatio-temporal coupling between ground-cover microhabitats (herb, bryophyte, and litter patches) and seedling regeneration. Based on these observations, Statistical methods, including ANOVA, multiple comparisons, distribution fitting and likelihood ratio tests, were employed to analyze the differences in seedling regeneration density and its temporal dynamics among the three microhabitats. The results showed that: (1) seedling density in herb microhabitats (87.5 ± 13.6 seedlings·m⁻²) was significantly higher than those in bryophyte (40.9 ± 6.9 seedlings·m⁻²) and litter microhabitats (31.0 ± 4.4 seedlings·m⁻²) (P < 0.01), while the difference between the latter two was not significant (P > 0.05); (2) the temporal dynamics of seedling emergence in herb microhabitats differed significantly from those in bryophyte and litter microhabitats (P < 0.01), with no significant difference between the latter two, and the peak period of seedling emergence in herb microhabitats occurred earlier and was more concentrated. Spatial heterogeneity of ground-cover microhabitats is a key factor driving the “seed-seedling transition paradox” and plays an important ecological role in the natural regeneration of P. schrenkiana var. tianschanica seedlings.