Yellow tomato (YT) is rich in nutrients and unique in flavour, its functional components need to be explored. Herein, we developed a fermented YT sauce product to explore its metabolic characteristics and probiotic potential. Results showed that YT paste had more functional components than red tomato one. The main metabolites of YT paste included Pro-Val-Glu-Thr-Leu, hypochlorous acid-3-sulfate and naringin, etc. During the fermentation of YT paste, its taste became richer. After fermentation, significant changes occurred in the metabolites of YT paste, with 306 metabolites significantly up-regulated, including β-galactosidase, S-phenyl-L-cysteine and S-adenosylmethionine and 34 oligopeptides, etc. The significant metabolic pathways involved were ABC transport, niacin and nicotinamide metabolism. The results of this study are expected to provide a reference for the deep processing and industrial development of YT.