Ulva prolifera, a type of marine macroalgae, is the causative species behind green tides mainly in the Yellow Sea and adjacent regions. Nevertheless, it can be used as food or animal feed in South China. The vegetative fragments of U. prolifera are an important seed source for successive green tide blooms. Fragmentation shortens the transition time from the vegetative state to the reproductive state. However, the translation of the algal metabolites during gametogenesis is far from well understood. In this study, the dynamic metabolic profiles of U. prolifera thallus during fragmentation-induced proliferation were investigated using non-targeted metabolomics approach via a series of time course experiments in June 2017. After a 30 min low temperature shock, fragmentation induced a reproductive response of 91.57% of U. prolifera in 48 h, whereas the value was only 21.43% in the control group. A total of 156 chromatographic peaks were detected, and 63 metabolites were significantly changed in U. prolifera during reproduction. Aanlysis of the kinetic metabolic pattern showed that the fragments not only induced the formation of sporangia, but also led to complex metabolite accumulation. During fragmentation-induced proliferation, U. prolifera consumed different sugars at different time points. γ-Aminobutyric acid (GABA), glutamic acid, gallic acid, and malic acid may play important roles in germ cell formation and in the release of U. prolifera, whereas n-hexanol, 2-methyl-3-phenylindole, and 3-indoleacetonitrile may be beneficial for biotic stress resistance. Compared with the control group, in the treatment group, metabolites such as alcohols and organic acids also showed significant difference with the photoperiod at the initial stage of proliferation (before 60 h). In conclusion, changes in the levels of metabolites, including sugars, organic acids, and alcohol with photoperiod may be the strategy adopted by U. prolifera to cope with fragmentation in nature.