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The determinants of food chain length (FCL), a crucial aspect of biodiversity due to its effects on ecosystem functioning, have long been debated. Previous studies proposed resource availability, disturbance, and ecosystem size as environmental drivers. However, studies using stable isotope approaches have shown inconsistent results, indicating missing links between environmental drivers and FCL. Here, we hypothesized that species richness and motifs (i.e. three‐species subgraphs) modulated environmental effects on FCL. Combining empirical food webs with ourN‐species food web model, we found that 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 internal food web structure should deepen our understanding of how FCL changes over environments.