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To enhance the nutrient removal efficiency of <i>Oocystis borgei</i> for mariculture wastewater (MW), the effects and processes of three phytohormones on nitrogen and phosphorus removal from synthetic mariculture wastewater (SMW) by <i>O. borgei</i> under sequential batch operation were compared. The findings revealed that the supplementation with 10⁻⁶ M 3-indoleacetic acid (IAA), gibberellic acid (GA3), and zeatin (ZT) resulted in the most effective elimination, while there was no appreciable difference among them. The nitrogen and phosphorus indices of the effluent dramatically reduced (<i>p</i> < 0.01) upon the supplementation of phytohormones, and the removal effects were ranked as NO₃⁻-N > PO₄³⁻-P > NH₄⁺-N > NO₂⁻-N. The removal rates for NH₄⁺-N and PO₄³⁻-P were 0.72–0.74 mg·L⁻¹·d⁻¹ and 1.26–1.30 mg·L⁻¹·d⁻¹, respectively. According to physiological studies, phytohormones enhanced the levels of photosynthetic pigments and chlorophyll fluorescence parameters (Fv/Fm and φPSII), thereby improving photosynthetic activity. Additionally, they stimulated Nitrate Reductase (NR) and Glutamine Synthetase (GS) activities to promote nitrogen metabolism and increased Superoxide Dismutase (SOD), Catalase (CAT), and carotenoid contents to mitigate oxidative stress damage caused by abiotic stress. These activities contribute to the proliferation of <i>O. borgei</i>, which in turn resulted in an increase in the assimilation of nitrogen and phosphorus from SMW. In conclusion, phytohormone supplementation significantly increased nutrient removal from SMW by <i>O. borgei</i> in a sequential batch reactor, which has potential application in MW treatment.