<p>Globally accelerating fish introductions and fisheries expansion in lacustrine ecosystems have imposed severe threats to endemic fish populations and ecological structures. Quantifying food web architecture and niche enables rigorous evaluation of invasive fishes’ roles in impacting endemic communities and their cascading ecosystem effects. Stable isotope analysis (<i>δ</i>¹³C and <i>δ</i>¹⁵N) of producers and consumers was combined using MixSIAR model to quantify the proportional contributions of basal carbon sources in Fuxian Lake. The trophic position estimation incorporated the carbon-source-weighted <i>δ</i>¹⁵N baselines, accounting for isotopic variability in source materials. Multidimensional datasets (carbon source contributions, trophic positions, isotopic niches, and life-history traits) were integrated to quantify the ecological impacts exerted by invasive species on endemic <i>Anabarilius grahami</i> populations. Results indicated pelagic carbon sources dominated (57.8%) the food web’s energy base. Furthermore, the food chain spanned 3.84 trophic positions, with the invasive <i>Pelteobagrus fulvidraco</i> as the apex predator. Isotopic niche analysis confirmed resource competition between the invasive <i> Neosalanx taihuensis</i> and <i>A. grahami</i>, with <i>N. taihuensis</i> exhibiting a 91.99% probability of occurring within the isotopic niche of <i>A. grahami</i> and <i>A. grahami</i> showing a 50.80% probability of overlapping with the isotopic niche of <i>N. taihuensis</i>. Simultaneously, the early life stages (eggs/juveniles) of <i>A. grahami</i> inhabiting nearshore rocks experienced high predation pressure from the invasive <i>Ctenogobius cliffordpopei</i> due to their littoral habitat overlap. This predation risk is corroborated by the invader’s elevated trophic position (Δ<i>δ</i>¹⁵N = 2.50‰) and isotopic congruence in basal carbon sources (Δ<i>δ</i>¹³C = 0.51‰). These synergistic mechanisms, resource competition and predation, collectively drive endemic population declines.</p>