The substitution of chemical nitrogen (N) fertilizer with organic fertilizer (organic substitution, OS) is increasingly applied in crop production, due to its environmentally friendly characteristics, low price, and high crop and soil improvement efficacies. Here, we studied the effects of chemical N fertilizer with organic fertilizer treatment at different proportions (no organic substitution (NOS), 20% (OS-20), 40% (OS-40), 60% (OS-60), 100% (OS-100), and 200% (OS-200, double the organic fertilizer application amount of OS-100) on the yield and quality of apples in the Shanxi Province of China. The results revealed that, compared to the NOS, the total apple yields of OS treatments, especially the OS-60 and OS-100 treatments, decreased. However, all OS treatments, except OS-200, increased the yield of large-sized fruits (transverse diameter ≥ 85 mm) and the mean mass of apple fruits, and significantly decreased yield of small-sized fruits (transverse diameter < 75 mm). All OS treatments, especially OS-40, promoted the total sugar and vitamin C (Vc) contents and fruit hardness of apples, and OS-40, OS-60, and OS-200 resulted in significantly decreased titratable acid contents in apples. The influence of organic substitutions on soil quality was further investigated in a two-year field experiment. The results showed that the influence of organic substitution on soil chemical properties differed between the two years. Notably, 40% OS increased the soil organic carbon (SOC) content and the C/N ratio in the upper 20 cm of the soil in both years. Additionally, OS treatments reduced the residual nitrate (NO3−)-N (RN) content in deep soil layers, suggesting that OS has the potential to alleviate N leaching. Moreover, redundancy analysis (RDA) of the soil, fruit yield, and fruit quality parameters revealed that the SOC content in the 0–20 cm soil layer and the RN content in the 0–100 cm soil layer had the greatest impact on the fruit quality and yield variables, respectively. This study showed that the proper substitution (40%) of chemical N fertilizer with organic fertilizer could improve the yield of large-sized fruits, the mean mass and fruit quality of apples, and soil chemical properties. Our study will provide a basis for rational organic substitution in apple orchards.