The olecranon honey peach is China’s national geographic identification product because of its crisp texture and high sweetness. In recent years, new field management practices have been developed. In this study, fruits (‘SJH’) grown through new planting methods, i.e., black bags combined with bio-organic fermentation fertilizer, were compared with those (‘SBY’) grown by conventional planting methods, i.e., using a chemical fertilizer without bagging, to determine their effects on improving fruit quality. At maturity, the ‘SJH’ was significantly higher than ‘SBY’ in terms of weight, hardness, and sugar content by 14.43%, 19.55% and 9.66%, respectively. RNA sequencing (RNA-seq) technology analysis was performed on ‘SJH’ and ‘SBY’ to identify the main regulatory pathways involved in fruit development, especially focusing on cell-wall biogenesis and sugar metabolism. We identified a total of 1660 differentially expressed genes (DEGs) in ‘SJH’ and 5673 genes in ‘SBY’ throughout the development. A clustering analysis of DEGs revealed that the expression patterns of key genes involved in cell-wall biogenesis and sugar metabolism pathways in ‘SJH’ differed from those in ‘SBY’, such as cellulose synthase-like protein D (CS-LPD), sucrose-phosphate synthase (SPS) and sucrose synthase (SUS). The new cultivation technology promoted soluble sugar accumulation and cell-wall synthesis through molecular regulation, which improved the sweetness and sensory quality of the fruit. These findings contribute towards to the development of novel ideas for the better cultivation of peaches and provide a deeper investigation into the molecular mechanism of their development.