The objective of this experiment was to compare the effect of atmospheric NH3 and N levels in a hydroponic solution on the chlorophyll fluorescence of two corn genotypes with different nitrogen use efficiencies. The hydroponic experiments were carried out in open top chambers. Chlorophyll fluorescence measurements were made at the seedling stage. The results showed that the Fo value of the two corn genotypes was not significantly affected by nitrogen levels in the hydroponic solution or increased atmospheric NH3 concentrations. Both the Fm and the Fv value of the high nitrogen use efficiency genotype (NE5) were significantly (p<0.05) lower in the high solution N + high atmospheric NH3 treatment compared to the high solution N + normal atmospheric NH3 treatment. In contrast, Fm and Fv of the low nitrogen efficiency genotype (SD19) were significantly higher in the high solution N + high atmospheric NH3 treatment compared to the high solution N + normal atmospheric NH3 treatment. Both Fm and Fv in the low solution N + high atmospheric NH3 treatment were lower compared to the high solution N + increased atmospheric NH3 treatment. This indicated that at high solution N levels, increased atmospheric NH3 concentrations had a negative effect on NE5, but a positive effect on SD19. The results also showed that the qN and qP value of the two corn genotypes decreased under different nitrogen levels and increased atmospheric NH3 concentrations. This indicated that the protection function of crops on photosynthesis was lower under high atmospheric NH3 compared to normal atmospheric NH3 concentrations.