(1) Background and Aims: Manure is an important source of nutrients for plants, and organic substrate, as an effective soil amendment substrate, is a common material for maintaining soil health in the context of agricultural intensification. The use of organic fertilizers to meet the nutrient requirements of crops and to improve soil structure is a natural choice for sustainable agriculture. The high cost of chemical fertilizers and their overuse can lead to agricultural pollution, so farmers’ awareness of organic farming is increasing, which is helping to drive agriculture in a more environmentally friendly and sustainable direction. (2) Methods: In a fertilization experiment conducted on 38-year-old ‘Changfu No.2’ apple trees, four different fertilization treatments were designed to assess their effects on soil fertility, fruit quality, and apple yield. These treatments included no fertilizer as a control (CK); chemical fertilizer combined with organic substrate (NPK + O); chemical fertilizer combined with sheep manure (NPK + SM); and a combination of chemical fertilizer, organic substrate, and sheep manure (NPK + O + SM). Principal component analysis (PCA) was used to comprehensively evaluate soil fertility, apple yield, and quality under these treatments. (3) Results: The NPK + O + SM treatment significantly improved soil fertility and apple yield compared to the other treatments. It provided comprehensive nutrition, meeting the diverse needs of plant growth. The slow-release properties of the organic substrate combined with the immediate nutrient supply from the sheep manure ensured stable nutrition throughout the growing season. This mixed fertilizer also improved soil biological activity. (4) Conclusion: The fertilization strategy combining organic substrate and sheep manure (NPK + O + SM) is highly effective in improving soil fertility, fruit quality, and apple yield, thus supporting sustainable agricultural practices.