This study aimed to evaluate the effects of specific LED light spectra on the growth and physiology of Changchuan No. 3 Capsicum annuum L. seedlings. The experimental design involved exposing pepper seedlings to six different spectral light combinations for 7, 14, and 21 days, with the treatments consisting of 2R1B1Y (red/blue/yellow = 2:1:1), 2R1B1FR (red/blue/far-red = 2:1:1), 2R1B1P (red/blue/purple = 2:1:1), 4R2B1G (red/blue/green = 4:2:1), 2R1B1G (red/blue/green = 2:1:1), and 2R1B (red/blue = 2:1). The results demonstrated distinct spectral regulation of seedling development: compared to the white light (CK), the 2R1B1FR (far-red light supplementation) treatment progressively stimulated stem elongation, increasing plant height and stem diameter by 81.6% and 25.9%, respectively, at day 21, but resulted in a more slender stem architecture. The 2R1B1G (balanced green light) treatment consistently promoted balanced growth, culminating in the highest seedling vigor index at the final stage. The 2R1B1P (purple light supplementation) treatment exhibited a strong promotive effect on root development, which became most pronounced at day 21 (126% increase in root dry weight), while concurrently enhancing soluble sugar content and reducing oxidative stress. Conversely, the 2R1B1Y (yellow light supplementation) treatment increased MDA content by 70% and led to a reduction in chlorophyll accumulation, while 2R1B (basic red–blue) resulted in lower biomass accumulation compared to the superior spectral treatments. The 4R2B1G (low green ratio) treatment showed context-dependent outcomes. This study elucidates how targeted spectral compositions, particularly involving far-red and green light, can optimize pepper seedling quality by modulating photomorphogenesis, carbon allocation, and stress physiology. The findings provide a mechanistic basis for designing efficient LED lighting protocols in controlled-environment agriculture to enhance pepper nursery production.