Apples at different ripening stages display distinct processing properties and browning characteristics in products. This study aimed to identify differential metabolites and metabolic pathways of browning pulp and browning inhibition pulp of Fuji apple across four ripening stages (M1–M4), corresponding to days after full bloom (DAFB: 148, 155, 162, and 171). We investigated the physicochemical characteristics, browning-related enzyme activities, and metabolomic profiles of apples at the four stages, revealing defensive metabolic changes associated with browning throughout ripening. Specifically, the browning rate in apples increased with ripening, peaking before declining in the late stages, and exhibited positive correlations with activities of polyphenol oxidase (PPO), peroxidase (POD), and catalase (CAT), and negative correlations with superoxide dismutase (SOD), phenylalanine ammonia-lyase (PAL), and H2O2 levels. Metabolomic profiling identified 315, 393, and 243 distinct metabolites in fresh control (FC), browning pulp (BR), and browning-inhibited pulps (CM) of apple at the four ripening stages, respectively. KEGG enrichment analysis revealed that FC and BR of the four ripening apples were differentiated by phenylpropanoid biosynthesis, while CM was featured by flavonoid biosynthesis. The characterized differential metabolites in BR were changed to α-linolenic acid metabolism with ripening, while those in CM were from flavonoid and phenylpropanoid biosynthesis. Furthermore, the in-depth analysis revealed 40 significantly differential metabolites associated with amino acid, nucleotide, coenzyme, and vitamin metabolism, potentially modulating the stress-responsive cellular redox balance. This research provides critical insights for browning prevention in the processing of fruits at various ripening stages.