Understanding the mechanisms of intra-climatic zonation ecological differentiation ("co-climatic ecological divergence") in lake ecosystems represents a pivotal scientific challenge in limnology. While climatic homogeneity is often presumed to drive uniform ecosystem functioning, our study demonstrates that under identical arid/semi-arid climatic regimes, divergent C-N nutrient cycling pathways may emerge due to heterogeneous lake morphometry, hydrological connectivity gradients, and anthropogenic pressures within coupled socio-ecological systems. This study investigated two typical lakes in northern China-algae-dominated Hulun Lake and macrophyte-dominated Ulan Nur Lake-by integrating stable isotopes (delta 13C, delta 15N), multi-parameter water quality data, and structural equation modeling (SEM). Our results highlight distinct nutrient pathways in two representative lakes: (1) Hulun Lake is dominated by allochthonous inputs, characterized by depleted delta 13C in suspended particulates (-25.31 f 2.49 %o) and delta 15N in sediments (5.42 f 3.27 %o), reflecting external nitrogen retention and hypoxia. (2) Ulan Nur Lake is regulated by internal metabolism, indicated by stable delta 13C signatures (-24.94 f 1.24 %o) from macrophyte cycling and enriched delta 15N in sediments (8.27 f 1.94 %o), consistent with long-term nitrogen recycling and low Total Nitrogen (TN) concentrations (1.94 f 0.76 mg/L). (3) Structural equation modeling (SEM) demonstrates that temperature (beta = 1.131) and external nitrogen input (beta = 0.444) are the dominant drivers of C-N pathway divergence through thermodynamic regulation and trophic cascade effects. Collectively, these findings reveal lake-type-dependent nutrient partitioning and support dual-pathway restoration strategies. By uncovering mechanisms of co-climatic ecological divergence, this study provides a proof-ofconcept framework in arid and semi-arid lake ecosystems.