Kadsura coccinea (Lem.) is a woody wine plant with a peculiar fruit enriched in important health-promoting compounds. The non-editable part of the fruit, i.e., the seed and peel, represents more than 60% of the fruit and is considered a biowaste. This significantly restricts the development of the K. coccinea fruit industry. Clarifying the metabolic components of the different fruit parts can help to improve the utilization rate and valorization of K. coccinea. Herein, we evaluated K. coccinea fruit peel, pulp, and seed using widely-targeted metabolomics and quantified a set of 736 bioactive compounds from 11 major metabolite classes. The most prominent metabolite classes included lipids, amino acids, flavonoids, and lignans. Furthermore, our results emphasized a significant accumulation of flavonoids in pulp tissues, while alkaloids and lignans were abundant in peel and seed tissues, respectively. A total of 183 metabolites were differentially accumulated among the three tissues. Procyanidin C2, rutinoside, 2-hydroxyoleanolic acid, 5-hydroxymethyluracil, nootkatol, isoquercitrin, isohyperoside, quercetin-7-O-glucoside, hyperin, and rutin showed elevated accumulation in the peel. In the seed, kadsuralignan G, kadcoccilactone A, kadsuralignan H, lysoPE 20:5, iso-schisandrin ethyl alcohol, and kadangustin were significantly enriched. Our results highlight the diverse metabolome composition of K. coccinea fruit parts, which can be further exploited for its valorization in various industries.