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Herbicide-induced phytoplankton inhibition poses a serious threat to coastal biodiversity and ecosystem function. Although extensive studies employing single, gradient concentration exposure are beneficial to understand the response of phytoplankton communities in various habitats to herbicide stress, the knowledge obtained is difficult to objectively evaluate the response of communities to continuous, pulsing inputs of herbicides in situ marine ecosystems. Here, we analyzed the concentration and seasonal distribution patterns of herbicides in global coastal waters, and simulated this pulsing process through two-phase of atrazine exposure mesocosm experiment. The results indicated that, without exceeding the threshold for biomass collapse in phytoplankton community, the differentiation of community composition by ambient concentration of atrazine could gradually recover in the short term, but sustained, dose-dependent inhibition of biomass was produced. Pre-exposure was conducive to improve the average tolerance of phytoplankton community to atrazine, but subsequent input of high-does atrazine rapidly reduced community biomass, diversity, and the number of rare groups, leading to synchronous changes in bacterial community structure. Consequently, we assume that phytoplankton community have a certain resistance to ambient concentrations of herbicides, however, cyclic herbicide inputs (long-term low-dose and short-term high-dose) may cause more detrimental effects than single gradient exposure, ultimately leading to a large-scale decline in coastal primary productivity. These findings contribute to understanding the response patterns of marine primary producers under pulse herbicide inputs, as well as potential impacts on biogeochemical cycles.