To elucidate the mechanisms underlying yield formation in response to water and fertilizer management in traditional and modern foxtail millet varieties, a field experiment was conducted using the traditional cultivar Jingu 6 and the modern cultivar Changsheng 13. Three irrigation regimes (rainfed, pre-sowing supplemental irrigation, and full growth-stage irrigation) and two fertilizer levels (high and low) were implemented. Phenotypic traits, photosynthetic parameters, dry matter accumulation and translocation, photosynthate content, and yield were measured. Multivariate statistical analysis was performed to reveal the intrinsic factors responsible for yield differences between the varieties under varying water and fertilizer conditions. The results indicated that the traditional cultivar exhibited low yield potential but high stability, with minimal inter-annual variation and low sensitivity to water and fertilizer inputs. Under rainfed conditions, its yield decreased by 16.98-39.18 %, which was maintained primarily through optimized photoprotective mechanisms and pre-flowering dry matter allocation. In contrast, the modern cultivar showed high yield potential but poor stability, with yield increases ranging from 39.09 % to 272.42 % under conditions of high water and high fertilizer inputs. Its high yield depended on full growth-stage irrigation, achieved mainly through improved plant architecture, enhanced photosynthetic efficiency, and strengthened source-sink coordination. Therefore, traditional cultivars are suitable for rainfed dryland agriculture, whereas modern cultivars require reliable irrigation. Future breeding strategies should integrate the water-saving and stress-tolerance traits of traditional cultivars with the high-yield potential of modern cultivars to develop water-efficient and high-yielding hybrids, which is crucial for building a climate-resilient foxtail millet production system.