Understanding the underlying ecological processes that control plant diversity within (α-diversity) and among (β-diversity) forest gaps is important for managing natural forest ecosystems, and it is also a prerequisite for identifying the formation and maintenance mechanisms of forest plant communities. In this study, we focused on the interrelationships among habitat type (gap/non-gap plots), gap size, elevation and environmental factors, and we explored their effects on plant diversity (α-diversity and β-diversity). To do this, a total of 21 non-gap (i.e., closed canopy) plots (100 m2) and 63 gap plots, including 21 with large gaps (200–410 m2), 21 with medium gaps (100–200 m2) and 21 with small gaps (38.5–100 m2), were selected along an elevational gradient in a subalpine coniferous forest of southwestern China. Using structural equation models (SEMs), we analyzed how forest gaps affected plant diversity (α-diversity and β-diversity) along an elevational gradient. The results showed that (1) as elevation increased, unimodal patterns of α-diversity were found in different-sized gaps, and β-diversity showed a consistent sinusoidal function pattern in different-sized gaps. The gap size was positively related to α-diversity, but this effect disappeared above 3500 masl. Moreover, the patterns of α-diversity and β-diversity in non-gap plots were irregular along the elevational gradient. (2) SEMs demonstrated that many environmental factors, such as the annual mean air temperature (AMAT), ultraviolet-A radiation (365 nm, UV-A365), ultraviolet-B1 radiation (297 nm, UV-B297), moss thickness (MT), soil carbon/nitrogen ratio (C/N ratio), NH4-N and NO3-N, were significantly affected by elevation, which then affected α-diversity and β-diversity. The photosynthetic photon flux density (PPFD), UV-A365 and UV-B297 were significantly higher in plots with forest gaps than in the non-gap plots. Moreover, the PPFD and UV-A365 were positively and directly affected by gap size. Surprisingly, except for the NH4-N and the C/N ratios, the below-ground environmental factors showed little or no relationships with forest gaps. All of these effects contributed to plant diversity. Overall, the above-ground environmental factors were more sensitive to gap-forming disturbances than the below-ground environmental factors, which affected α-diversity and β-diversity. The predicted pathway in the SEMs of the elevational effects on α-diversity and β-diversity was relatively complicated compared with the effects of forest gaps. These results can provide valuable insights into the underlying mechanisms driving the diversity-habitat relationship in the subalpine coniferous forests of southwestern China.