There have been long-standing debates on the determinants of the food chain length (FCL), a vertical dimension of biodiversity. Previous studies have proposed three environmental factors as putative controls of FCL: resource availability, disturbance, and ecosystem size. However, field studies using stable isotope approaches have produced inconsistent results, suggesting missing links between environmental drivers and FCL. Here, we hypothesized that species richness and motifs (i.e., 3-species subgraphs) modulated environmental effects on FCL. Empirical food webs and our mathematical model of N-species food webs showed that FCL positively correlated with species richness and the 3-species chain motif. Although species richness had a stronger effect on FCL than the chain motif, FCL disproportionately changed at low species richness with saturation at high species richness. This functional response was essential to the interdependent effects of disturbance and ecosystem size in our model. Disturbance more strongly regulated FCL in smaller ecosystems, where species richness was low. Similarly, increasing ecosystem size enhanced FCL under strong, but not weak, disturbance regimes. Our study suggests that the current inconsistency among FCL research may be a natural outcome of inherent food web complexity. Considering internal food web structure should deepen our understanding of how FCL changes over environments.