Marine algae have excellent bioresource properties with potential nutritional and bioactive therapeutic benefits, but studies regarding Caulerpa lentillifera are limited. This study aims to explore the metabolites profile and the antioxidant, anticancer, anti-obesity, and in vitro cytotoxicity properties of fractionated ethanolic extract of C. lentillifera using two maceration and soxhlet extraction methods. Dried simplicia of C. lentillifera was mashed and extracted in ethanol solvent, concentrated and evaporated, then sequentially partitioned with equal volumes of ethyl acetate and n-Hexane. Six samples were used in this study, consisting of ME (Maceration—Ethanol), MEA (Maceration—Ethyl Acetate), MH (Maceration—n-Hexane), SE (Soxhletation—Ethanol), SEA (Soxhletation—Ethyl Acetate), and SH (Soxhletation—n-Hexane). Non-targeted metabolomic profiling was determined using LC-HRMS, while antioxidant, anti-obesity, and anticancer cytotoxicity were determined using DPPH and ABTS, lipase inhibition, and MTT assay, respectively. This study demonstrates that C. lentillifera has several functional metabolites, antioxidant capacity (EC50 MH is very close to EC50 of Trolox), as well as anti-obesity properties (EC50 MH < EC50 orlistat, an inhibitor of lipid hydrolyzing enzymes), which are useful as precursors for new therapeutic approaches in improving obesity-related diseases. More interestingly, ME, MH, and SE are novel bioresource agents for anticancer drugs, especially for hepatoma, breast, colorectal, and leukemia cancers. Finally, C. lentillifera can be a nutraceutical with great therapeutic benefits.