To obtain the compatibility of interstocks crossing with ‘Yuanxiaochun’, we performed a comparative analysis with five interstocks. From the 60th to 240th day after grafting, there was a significant difference between different treatments. All the new shoot/interstock diameter ratios were <1, indicating that there was no obvious phenomenon of small feet in ‘Yuanxiaochun’ seedlings of five kinds of interstocks. The density of ‘Yuanxiaochun’ was significantly different. Chl a, Chl b, T-Chl content of ‘Shiranuhi’, ‘Harumi’, ‘Tarocco’ changed greatly from the 90th to 120th day after grafting. The intercellular CO2 concentration (Ci) of ‘Shiranuhi’ was significantly higher than the other interstocks. In addition, when ‘Yuanxiaochun’ was grafted onto ‘Shiranuhi’, net photosynthetic rate (Pn), stomatal conductance (gs) and tanspiration rate (Tr) were higher. When ‘Harumi’ were used as the interstocks of ‘Yuanxiaochun’, the light saturation point (LSP) value was larger, which was conducive to the utilisation of strong light. Moreover, the value of LSP-LCP (LCP, light compensation point) of ‘Harumi’ and ‘Tarocco’ were significantly higher than the other three interstocks. The apparent quantum efficiency (AQE), RuBP maximum regeneration rate (Jmax) and maximum carboxylation efficiency of Rubisco (Vcmax) value of ‘Shiranuhi’ was significantly lower than that of ‘Ponkan’. The CO2 compensation point (CCP) of ‘Harumi’ interstock was lower, but the CO2 saturation point (CSP) of ‘Tarocco’ interstock was higher than those of other interstocks respectively. There was a small difference in initial fluorescence (F0) of different interstocks. The maximal photochemical efficiency of PSII in the dark (Fv/Fm) of ‘Kumquat’ was the lowest. In addition, Both Y(II) and ETR values of the ‘Yuanxiaochun’ leaves of ‘Ponkan’ interstock was the largest one. However, the non-photochemical quenching (qN) of ‘Ponkan’ was significantly lower, and that of ‘Tarocco’ interstock was the highest one. Interstocks have different effect on the growth and development, photosynthetic characteristics related to physiological characteristics of ‘Yuanxiaochun’ trees. ‘Ponkan’ and ‘Kumquat’ as the interstock of ‘Yuanxiaochun’ was more conducive to the rapid accumulation of photosynthetic products for normal vegetative and reproductive growth of plants.