Photosynthesis is an essential plant biological process. The performance of photosynthesis in grafted plants is affected by either the scion or the rootstock. However, the effect of the scion, rootstock and their interaction in the scion-rootstock combinations on photosynthesis of the grafted trees was not clear. In this research, the photosynthesis was analyzed within 21 citrus scion-rootstock combinations derived from three navel oranges (Citrus sinensis cv. 'Banfield', 'Chislett' and 'Powell') grafted on seven rootstocks [(Swingle citrumelo (C. paradisi × Poncirus trifoliata), Carrizo citrange (C. sinensis × P. trifoliata), X639 (C. reticulata × P. trifoliata), MXT (C. sinensis × P. trifoliata), Hongju (C. reticulata), Ziyang xiangcheng (C. junos) and Trifoliate orange (P. trifoliata)]. Results indicated that photosynthesis of these grafted citrus plants was significantly affected by all the scion, rootstock and their interaction. The rootstock and scion-rootstock interaction had more effect on both chlorophyll fluorescence and photosynthetic parameters with lower p values than the scion. All the scions grafted on Swingle showed the highest electron transport rate at 132.24, 158.39 and 154.59 µmol electrons m-2 s-1, and a higher net CO2 assimilation rate at 11.22, 10.77 and 11.69 µmol m-2 s-1, respectively. The rootstock is the predominant factor affecting the content of photosynthetic pigments, and the combinations using Ziyang xiangcheng as the rootstock had the highest content at 19.83, 20.97 and 20.39 μmol s-1 Kg-1 FW. Electron transport rate is probably the predominant factor determining the final photosynthesis of the grafted citrus trees. This research is the first to reveal the respective effect of the scion, rootstock and their interaction on photosynthesis of citrus scion-rootstock combinations and is valuable in enhancing the understanding of the different performances in citrus scion-rootstock combinations, which aids in selecting optimal scion-rootstock combinations.