The objective of the current study is to evaluate both the positive and negative effects of manganese-doped graphene quantum dots (GQD-Mn) on Capsicum annuum L. grown under salt stress. GQD-Mn was synthesized, characterized, and foliar-applied (250 mg/L, 120 mg/L, 60 mg/L) to C. annuum L. before and after the flowering stage, during which 100 mM of NaCl solution was introduced into the soil as salt stress. Controls were designed as absolute control (no nanomaterials or salt) and negative control (no nanomaterials only salt). Herein, we report that GQD-Mn offset the reduction of fruit production in salt-stressed C. annuum L. by around 40 %. However, based on a comprehensive analysis of normal alkanes (n-alkane) using gas chromatography-mass spectrometry (GC-MS), we also observed that the leaf epicuticular wax profile was disturbed by GQD-Mn, as the concentration of long-chain n-alkanes was increased. Meanwhile, the content of magnesium (Mg) and zinc (Zn) indicated a potential promoted photosynthesis activity in C. annuum L leaves. We hypothesize that the optical properties of GQD-Mn allow leaves to utilize light more efficiently, thus improving photosynthetic activities in plants to acclimate salt stress. But the increased light usage also induced heat stress on the leaf surfaces, which caused n-alkanes changes. Our results provided a unique perspective on nano-plant interaction that value both beneficial and toxic effects of nanomaterials, especially when evaluating the safety of nano-enabled agriculture in areas facing harsh environmental conditions such as salinity.