In order to provide a theoretical basis for the selection of suitable scionstock combinations of apple in the northwest Loess Plateau, we studied the growth, photosynthetic and fluorescence characteristics of different combinations. Malus halliana (CSHT) and Malus hupehensis (PYTC) were employed as rootstocks, and Malus pumila ‘Yanfu 6’ (Y6) and Malus pumila ‘Nagafu 2’ (C2) were used as scions, and the graft affinity, growth, photosynthesis, chlorophyll fluorescence characteristics and chlorophyll content (SPAD) of four combinations were measured. (1) The grafting affinity of CSHT+Y6 was the highest among four combinations for the diameter ratio was nearest to 1. (2) During the whole growth period, the growth, net photosynthetic rate (P_n), the maximum fluorescence (F_m), and photochemical efficiency (F_v/F_m) in the combinations of two scions on the Malus halliana were significantly higher than that of Malus huphensis, also the intercellular CO₂ concentration (C_i) and the initial fluorescence (F₀) of it were lower than that of M. huphensis. There is no significant difference in the photochemical quenching coefficient (qP) among the four scionstock combinations. (3) When the light intensity was higher in August, the stomatal conductance (G_s) of CSHT+Y6 was significantly higher than that of other combinations. The transpiration rate (Tr) and chlorophyll content (SPAD) of the two scions on the M. halliana were higher than that of M. huphensis. (4) The indices were comprehensively evaluated using the principal component analysis. According to the comprehensive score of the four combinations, the order was from high to low: CSHT+Y6, CSHT+C2, PYTC+C2 and PYTC+Y6. Therefore, the resistance of M. halliana is better than that of M. huphensis. CSHT+Y6, which was a suitable combination in central Gansu province, possessed the highest grafting affinity, the best growth and great photosynthetic capacity.