Auxenochlorella pyrenoidosa, a promising edible bioresource, can be efficiently and safely cultivated using exogenous phytohormones to enhance its productivity. This study employed multi-omics analysis to systematically investigate the effects and mechanisms of exogenous trans-Zeatin (tZ) on the growth and metabolism of A. pyrenoidosa. Results demonstrated that 10 mg/L tZ significantly promoted algal growth, increasing biomass by 166 ± 3.35% at 72 hours (h), while concurrently elevating cellular soluble protein (SP), carbohydrate (CHO), and chlorophyll a (Chla) content. tZ also strengthened the antioxidant defense system, evidenced by reduced reactive oxygen species (ROS) levels, enhanced activities of antioxidant enzymes (superoxide dismutase (SOD) and catalase (CAT)), upregulation of glutathione metabolism, and decreased lipid peroxidation product (malondialdehyde (MDA)). Furthermore, tZ activated key metabolic pathways, including nitrogen metabolism, photosynthetic carbon fixation, and porphyrin biosynthesis, leading to the accumulation of arginine and polyamines, etc. This study reveals that tZ promotes microalgal growth by coordinately regulating carbon–nitrogen metabolic networks and antioxidant systems, providing a theoretical foundation for phytohormone-augmented microalgae cultivation technologies.