This study investigates the lipid-lowering potential of Synsepalum dulcificum Daniell (miracle fruit) kernels using zebrafish models. Bioactivity-guided fractionation identified ethyl acetate (EA) and n-butanol (NB) fractions as significantly reducing the level of lipid accumulation. Phytochemical analysis led to the isolation of nine compounds, including five novel triterpenoid glycosides (1–5) and one new coumaroylethanolamine glycoside (6) from the NB fraction, alongside flavonoids (7–8) and a triterpenoid-coumaroyl conjugate (9) from the EA fraction. Compounds 1–5 and 7 demonstrated potent dose-dependent reductions in triglyceride (TG) and total cholesterol (TC) at the phenotypic level. The Q-PCR experiment showed that the active compounds upregulated the expression of PPARγ and AMPKα1, while they downregulated the expression of FAS. Structure–activity relationships indicated glycosylation patterns critically influence efficacy. This study first reports novel triterpenoid glycosides from miracle fruit kernels with significant lipid-lowering activity for functional foods.