The relationship between nitrogen (N) sources and photosynthetic capacity of leaf differs between species. However, the leaf anatomical variabilities related to photosynthesis ( A) of shrubs under different forms of N remain imperfectly known. Here, Lonicera Japonica (a shrub) was grown hydroponically in the presence of three forms of N (sole NH 4 +, 50%/50% NH 4 +/NO 3 – and sole NO 3 –). A and photosynthetic N use efficiency significantly decreased under sole NH 4 + supply, in parallel with down-regulated stomatal conductance ( g s), mesophyll conductance ( g m), and electron transfer rate ( J). Up to the total A decline of 41.28% in sole NH 4 + supply (compare with sole NO 3 –), the g m attributed to 60.3% of the total limitations. Besides, the decreased internal air space explained the increase of gas-phase resistance, and the increased liquid-phase resistance in sole NH 4 + supply was ascribed to the thicker cell wall thickness ( T cw) and decreased chloroplasts exposed surface area per unit leaf area ( S c/ S). The discrepancy of S c/ S could be interpreted by the altered chloroplasts numbers and the distance between adjacent chloroplasts ( D chl-chl). These results indicate the alteration of T cw and chloroplast numbers were the main causes of the difference in g m in coping with varied N sources.