Carotenoids are indispensable for human health, and citrus fruit are a crucial source of dietary carotenoids. Bagging, an important orchard practice to enhance fruit economic value, is widely used in many horticultural crops, including citrus fruit. The bagged ‘Majiayou’ pomelo (Citrus grandis) produces vivid deeper red pulp, a fantastic agronomic trait, but the underlying molecular regulatory mechanism remains largely unexplored. Here, the enhancement of carotenoids, especially lycopene, was confirmed by HPLC analysis of carotenoids in the pulp of bagged fruit and controls. qRT-PCR analysis of the 14 carotenoid pathway genes further revealed that upregulated PSY and downregulated CCD1 expression in bagged fruit could directly enhance the accumulation of carotenoids. In addition, RNA-seq analysis identified 311 differentially expressed genes (DEGs) in the bagged fruit and controls in five developmental stages. Weighted gene co-expression network analysis (WGCNA) identified 13 critical candidate genes among the DEGs, which are closely associated with lycopene accumulation. The underlying regulatory mechanism of these candidate genes on the transcription of carotenoid pathway genes in the bagged fruit was discussed. Considering that the candidate genes were involved in the corresponding metabolic pathways, the increase in sucrose content and decrease in ABA in bagged fruit were also identified, implying that these candidate genes may indirectly related to carotenoid enhancement in pulp by regulating phytohormones, primary metabolism, and stress responses. The results provide new insights into the potential regulatory mechanism of lycopene enhancement in the pulp of bagged ‘Majiayou’ pomelo, facilitating breeding and orchard management efforts to improve the nutritional quality and aesthetic value of citrus, and perhaps other fruit crops.