Quality deterioration due to undesirable discolorations in crude pine oleoresin during storage is a major problem limiting its subsequent processing applications. To reveal the essence of color changes, the browning phenomenon and comprehensive mechanism of crude pine oleoresin during storage were investigated in depth using an approach based on high-resolution mass spectrometry metabolomics. Crude pine oleoresin was stored with sterile, deionized, tap, and pond water for 30, 60, 90, 120, 150, and 180 days, respectively. The changes in browning substrate were detected by tracking analysis protein, reducing sugar, ascorbic acid, and total phenol content, browning was evaluated through colorimeter measurement. The metabolism of crude pine oleoresin in different storage times was uncovered that total color difference (ΔE) increased with storage time, and the browning of crude pine oleoresin soaked in tap water was greatest while soaked in deionized water exhibited the mildest. The content of reducing sugars, proteins, and total phenols increased with storage time, whereas the ascorbic acid content tended to increase and then decrease. Furthermore, the metabolomics analyses showed that 1,194 and 979 differentially metabolized compounds were found between days 120 and days 150, and days 120 and days 180. The metabolite profiles in the water samples changed as crude pine oleoresin storage time increased. Most carbohydrate content decreased, and the phenols and organic acids content increased. Metabolic network mapping linking differentially metabolized compounds by mapping different biosynthetic pathways proved that caffeoylquinic acid and catechin play a key role in the browning of crude pine oleoresin during storage: caffeoylquinic acid forms black iron complexes with iron, and catechin is oxidized to catechol quinone, which eventually produces a yellow dimer. This study will provide a scientific basis for developing or choosing more effective methods for controlling the discoloration of crude pine oleoresin and other similar products during storage.