Pepper (Capsicum annuum L.) is an important economic crop whose yield and quality are heavily influenced by fertilization management. However, varietal differences in response to different fertilization regimes and the underlying mechanisms remain unclear. In this study, we systematically analyzed the effects of five fertilization treatments-compound fertilizer (CK), single-element NPK fertilizer, NPK combined with organic fertilizer, reduced N, and increased N-across four pepper varieties. We measured soil total N, P, K and organic matter, and assessed plant biomass distribution and fruit quality (capsaicin and capsanthin contents). Results showed that fertilization significantly altered soil nutrient levels, especially nitrogen, with marked differences among varieties and treatments. Dan Sheng 52 exhibited the highest N-uptake efficiency under both NPK and organic fertilizer treatments, while Qian Jiao 8 achieved optimal P-uptake efficiency under reduced N. Potassium dynamics were complex, but the mixed NPK-organic fertilizer treatment promoted K uptake in certain varieties. Fruit-quality analysis revealed that capsaicin and capsanthin accumulation were jointly influenced by fertilization and genotype: Dan Sheng 52 under the CK treatment had significantly higher capsaicin than other treatments, indicating that adequate N supply promotes capsaicin synthesis; by contrast, Qian Jiao 8 receiving NPK fertilizer showed the highest capsanthin content, highlighting the critical role of optimized fertilizer ratios in pigment accumulation. Genotypic variation in metabolic responses under identical fertilization conditions underscores the need for precision management. Tailoring fertilizer type and ratio to varietal traits can enhance nutrient-use efficiency, improve fruit flavor and nutritional value, and provide a theoretical basis for precision fertilization and high-efficiency pepper production.