Molecular nutrition study is essential for assessing food quality. Pyropia haitanensis is nutritious and delicious health food in southern China. Consumers prefer the first harvested P. haitanensis for its tender taste. To understand the comprehensive alteration in the nutrition of P. haitanensis with different harvest time, we characterized the metabolomic variations induced by harvest time using NMR spectroscopy coupled with multivariate data analysis.We found that harvest time was an important factor influencing the nutrient composition of P. haitanensis. The levels of glutamine, alanine, aspartate, taurine, and isofloridoside contained in seaweeds were significantly increased over the harvest time. These findings enhanced our understanding of the nutritional features of P. haitanensis harvested at different times and provided useful information on the quality assessment of P. haitanensis.