Duckweed species are nutritionally meaningless plant which grow wildly in unattended areas. Therefore, understanding the metabolites content in duckweed species is essential for designing a future food products. Here, we report an untargeted Gas Chromatography-Mass Spectrometry (GC-MS)-based metabolomics approach for comprehensively discriminating between Lemna minor and Wolffia globosa of duckweeds species using principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA). Ten differential metabolites levels were tentatively identified between L. minor and W. globosa. Relative to W. globosa, L. minor appeared to enrich with 5-Hydroxyl-L-tryptophan, Tocopheryl acetate, Naringenin, α-linolenic acid and glutamic acid. Furthermore, the nutritional and microbial analyses of ice cream formulated with dried L. minor were investigated. The nutritional analysis results show that relative to control, the ice cream with 2% dried L. minor had significantly increased protein, fiber and ash content. In addition, total plate count (TPC) for microbial analysis of duckweed ice cream was performed. The result suggested that the small amount of bacteria (3.82 cfu/g) was traced in formulated ice cream with 2% dried L. minor. Overall, the metabolites profile, nutritional and microbial analyses of food used L. minor plant indicate that duckweed is a good candidate for future food.