Abstract: Orchard ecosystems are an important form of agriculture that plays a significant role in the carbon sink of terrestrial ecosystems in China. Estimating carbon sequestration and economic value of orchards is a central part of global carbon cycle research. In this study, six orthogonal combinations of three stock species (Malus micromalus, M. baccata, and M. hupehensis) and two scions of apple cultivars ('Fuji' and 'Golden Delicious') were examined for the carbon storage in the vegetation layers, soil, and litter of apple orchard. Carbon storage in the orchard ecosystems was summarized, and the carbon sequestration capacities of different soil-vegetation systems were explored. This work provides a theoretical basis for improving the carbon storage of apple orchards. The results showed that, compared with other tissues, the roots had the highest carbon content, while the trunk biomass was the highest among all organs biomasses, accounting for 33.89% to 47.95% of the total biomass. The carbon storage of each organ was different and in the sequence of trunk > branches > root. Carbon storage in the trunk accounted for more than 38% of the whole plant. When comparing the plant carbon storage of each combination, there were significant differences between scions. When M. baccata and M. hupehensis were used as stocks, the combination with 'Fuji' as the scion was significantly higher than that with 'Golden Delicious'. Comparison of the litter carbon storage in the various stocks and scions showed significant differences between different scions of the same stock; the stock combination with 'Fuji' was significantly higher than the combination with 'Golden Delicious'. Carbon storage in the litter indicated that there were significant differences in carbon storage among stocks. Carbon storage in the litter of combinations with M. baccata as the stock was significantly higher than in the combinations with M. micromalus and M. hupehensis as stocks. However, there were no significant differences between the latter two. Carbon storage in the 0-20 cm soil layer (57.86-80.91 t·hm^-2) was significantly higher than that in the 20-40 cm (20.15-25.97 t·hm^-2), 40-60 cm (11.54-14.62 t·hm^-2), and 60-100 cm (17.41-33.98 t·hm^-2) soil layers. 'Golden Delicious'/M. baccata had the highest carbon storage value per area. Moreover, there was little difference in the economic value of carbon storage in each stock combination, with an average of RMB 170.84 thousand Yuan per hectare.