Sucrose synthase (SuSy, EC 2.4.1.13) is a unique glycosyltransferase (GT) for developing cost-effective glycosylation processes. Up to now, some SuSys derived from plants and bacteria have been used to recycle uridine 5’-diphosphate glucose in the reactions catalyzed by Leloir GTs. In this study, after sequence mining and experimental verification, a SuSy from Micractinium conductrix (McSuSy), a single-cell green alga, was identified. In the direction of sucrose cleavage, the optimum temperature and pH of the recombinant McSuSy were 60 °C and pH 7.0. The mutations of the predicted N-terminal phosphorylation site (S31D) and the QN motif (K684T and N685D) significantly stimulated the activity of McSuSy. When the mutant S31D/684T/685D of McSuSy, with the highest activity, was applied by coupling the engineered yeast glycosyltransferase UGT51 in a one-pot two-enzyme reaction, 8 mM protopanaxadiol was transformed into 6.02 mM (3.75 g/L) ginsenoside Rh2 within 3 h at 37 °C. The yield was comparable to the control reaction of AtSuSy1 from Arabidopsis thaliana. This work reveals the lower eukaryotes as a promising resource for SuSys of industrial interest.