Field experiments were conducted in two locations in China to determine the effects of nitrogen (N) deficiency on plant growth and leaf photosynthesis of two super hybrid rice cultivars grown under no-till direct seeded conditions. Results showed that total dry mass was reduced by 39–48% in N-deficient plants. Leaf area index was decreased by 45–58% under N-deficient conditions. Less leaf number per unit land area resulting from reduced tiller number per unit area and small leaf size were responsible for the small leaf area index in N-deficient plants. N-deficient plants had 19–26% lower leaf N content and 7–12% lower relative chlorophyll content in flag leaves. In parallel with this, net photosynthetic rate and stomatal conductance were decreased by 14–24% and 14–42%, respectively, in N-deficient plants. However, the depression of stomatal conductance did not explain the lower photosynthetic capacity because intercellular CO2 concentration was not definitely reduced in N-deficient plants. Our results highlight the need for greater fundamental understanding of the effects of N deficiency on mesophyll function in no-till direct seeded super hybrid rice.