Ecological scale has been widely assumed to influence various biodiversity-productivity relationships in ecological communities; however, its robustness has not been extensively studied. In this study, we tested the scale dependency of biodiversity-productivity relationships by evaluating their direct linkages while considering other confounders, and simultaneously incorporating functional traits and interspecific phylogenetic relationships. We surveyed sixty quadrats each with an area of 0.25 m2 in three different meadows located along an elevational gradient in Yulong Mountain, China. We calculated different biodiversity parameters (richness, evenness, functionality, and phylogeny), and evaluated the chemical properties of soil from all quadrats, correlating their relationships with plant productivity at the local and regional scale. The direct and indirect relationships of biodiversity and productivity were evaluated using structural equation modeling. The biodiversity-productivity relationships were weak and inconsistent at the local scale, whereas some biodiversity metrics (richness, functional, and phylogenetic) showed either strong positive or negative relationships with productivity at the regional scale. However, a direct correlation between productivity and variables such as soil pH and community-weighted mean leaf carbon content was observed in the structural equation model reconstructed. Our study indicates that the scale dependency of biodiversity-productivity relationships in natural habitats may not be as strong as it may have been previously perceived, in case of taxonomic, functional, and phylogenetic diversity, respectively. Our study emphasizes the necessity to account for the confounding effects of abiotic factors when evaluating biodiversity-productivity relationship in natural habitats at regional or even worldwide scales.