A mass mortality often occurs from molting to the megalopa stage during the larval development of the swimming crab Portunus trituberculatus. Larvae with insufficient nutrient accumulation during the zoeal stages are probably unable to develop into juvenile swimming crabs. However, the nutritional information such as the primary metabolites is scarce for P. trituberculatus larvae. The aim of this work is to obtain an insight into the metabolite traits of P. trituberculatus at early developmental stages. 1 H nuclear magnetic resonance spectroscopy coupled with multivariate data analysis was used to determine how the metabolite profiles shift during larval development in P. trituberculatus. Our results show that the trend of total metabolites exhibited a rise from zoea 1 to zoea 3, followed by a drop from zoea 4 to megalopa and recovery during the first juvenile stage. A large-scale depletion of total metabolites in the zoea 4 and megalopa stages suggests a deep depression of metabolic activity, which may be linked to the mass mortality from molting to the megalopa stage. These findings provided essential metabolic information about the larval development of P. trituberculatus and important clues for understanding the nutritional requirements of P. trituberculatus in early developmental stages.