Through integrated multi-omics analysis, two phosphoenolpyruvate carboxylase genes, SaPEPC1 and SaPEPC2, were identified in Suaeda aralocaspica. SaPEPC1 was strongly induced by light, whereas SaPEPC2 showed little sensitivity to changes in light intensity. Moreover, SaPEPC1 consistently exhibited higher expression levels than SaPEPC2. To further investigate their functions, both genes were overexpressed in Arabidopsis. Overexpression of SaPEPC1 resulted in a marked increase in shoot fresh weight and leaf length, which was accompanied by thicker palisade and spongy mesophyll tissues. Under intense-light conditions, SaPEPC1 transgenic lines displayed enhanced activation of starch and sucrose metabolism, characterized by an increased number and expanded surface area of starch granules per cell, as well as enhanced chloroplast division. In contrast, SaPEPC2 overexpression had no significant effect on these traits. Joint transcriptome-metabolome analysis further revealed that sucrose metabolism-related genes (AtSUS6, AtBAM5, AtBGLU6) were expressed at significantly higher levels in SaPEPC1-overexpressing lines compared with both wild-type (WT) and SaPEPC2 transgenic plants under intense light. These results suggest that SaPEPC1 primarily regulates photosynthetic carbon assimilation and promotes carbohydrate accumulation, whereas SaPEPC2 is involved in basal metabolic processes. Under weak light conditions, both SaPEPC1 and SaPEPC2 transgenic lines exhibited reduced tricarboxylic acid (TCA) cycle activity. Overall, these findings identify SaPEPC1 as a key gene driving photosynthesis in S. aralocaspica, while SaPEPC2 contributes only marginally to this process. The mechanistic basis for their functional divergence, however, requires further investigation.