Elevated [CO₂] enhances light interception and carboxylation efficiency in plants. The combined effects of [CO₂] and photosynthetic photon flux density (PPFD) on stomatal morphology, leaf anatomy, and photosynthetic capacity in tomato seedlings remain unclear. This study subjected tomato seedlings (Solanum lycopersicum Mill. cv. Jingpeng No.1) to two [CO₂] (ambient [a[CO₂], 400 µmol·mol⁻¹] and enriched [e[CO₂], 800 µmol·mol⁻¹]) and three PPFD levels (L; low[Ll: 200 µmol·m⁻²·s⁻¹], moderate[Lm: 300 µmol·m⁻²·s⁻¹], and high[Lh: 400 µmol·m⁻²·s⁻¹]) to assess their interactive impacts. Results showed that e[CO₂] and increased PPFD synergistically improved relative growth rate and net assimilation rate while reducing specific leaf area and leaf area ratio. Notably, e[CO₂] decreased stomatal aperture (−13.81%) and density (−27.76%), whereas elevated PPFD promoted stomatal morphological adjustments. Additionally, Leaf thickness increased by 72.98% under e[CO₂], with Lm and Lh enhancing this by 10.79% and 41.50% compared to Ll. Furthermore, photosynthetic performance under e[CO₂] was further evidenced by improved chlorophyll fluorescence parameters (excluding non-photochemical quenching). While both e[CO₂] and increased PPFD Photosynthetic performance under e[CO₂] was further evidenced by improved chlorophyll fluorescence parameters (excluding non-photochemical quenching). Moreover, e[CO₂]-Lh treatment maximized total dry mass and seedling health index. Correlation analysis indicated that synergistic optimization of stomatal traits and leaf structure under a combination of e[CO₂] and increased PPFD enhanced light harvesting and CO₂ diffusion, thereby promoting carbon assimilation. These findings highlight e[CO₂]-Lh as an optimal strategy for tomato seedling growth, providing empirical guidance for precision CO₂ fertilization and light management in controlled cultivation.