Shrub encroachment and soil respiration (SR) are predicted to increase in the tundra ecosystem under climate warming, but little is known regarding potential causal relationships between shrubs and SR at a local scale. Multiple and complex belowground processes exist between the two phenomena, and consolidation is logistically difficult. Our study aimed to identify and integrate multiple belowground processes to elucidate the impact of shrub coverage on SR, using structural equation modeling (SEM). Results indicated that shrub coverage enhanced SR through root biomass, fungal community composition and soil temperature. SEM also revealed a potential indirect effect via interactions among those soil factors. Soil factors relating heterotrophic respiration affected on SR through more complex interaction among the factors. However, total effect sizes on SR were similar between factors relating autotrophic respiration and that relating heterotrophic respiration, suggesting that SR increases with shrub coverage would be unlikely to result from decreases in soil organic matter.