The production of biodiesel using microalgae has emerged as a promising alternative to fossil fuel-derived energy. However, microalgae-based biodiesel still faces challenges in achieving commercial economic feasibility. One of the primary reasons for this challenge is the limited extraction yield of long-chain fatty acids (LCFAs), which are essential for biodiesel synthesis. This study explores an easily accessible ozone-based extraction method to maximize LCFAs yields to address limitations. The experiments were conducted using Chlorella vulgaris, and the extraction efficiency was assessed for single ozone treatment and the combination of ozone treatment with physical (ultrasound) and chemical (pH adjustment) methods. The results indicated that LCFAs yield (33.12 mg/g) was achieved at 5 mg/L ozone concentration for 15 min at neutral pH, which was 3.41 times higher than that of the control (9.71 mg/g). Furthermore, combining ozone treatment with 100 W of ultrasound further enhanced the LCFAs yield to 52.32 mg/g, demonstrating a synergistic effect between ozone and physical treatment. The mechanism behind the increased extraction efficiency was attributed to the weakening of the cell wall, which facilitated LCFAs extraction. Additionally, it was observed that endogenous lipid synthesis was enhanced when the antioxidant 2,4-di-tert-butylphenol (2,4-DTBP) was promoted in response to oxidative stress. The extracted LCFAs in this study were mainly saturated fatty acids, namely palmitic acid (C16:0) and stearic acid (C18:0). This study offers insights into optimizing ozone-based LCFA extraction as a scalable, eco-friendly method for microalgal biodiesel production, emphasizing its potential to reduce carbon dioxide emissions and support carbon-neutral energy solutions.