In this study, it was investigated to increase the lipid yield of the microalgae Schizochytrium sp., by applying different cell disruption methods. Therefore, acid treatment with HCl, osmotic shock, enzyme applications and ultrasonic homogenizer were tried in this algae species combined with the Bligh and Dyer and Soxhlet methods as an alternative to classical lipid extraction methods. As a result of the study, the highest lipid value (21.72 ± 0.74%) was obtained in enzyme application with Bligh and Dyer method (BDE). The cell disruption processes increased the lipid yield compared to the control groups. The highest PUFA DHA was found in the range of 4.58 ± 2.44-19.25 ± 0.09%, and the highest value was observed in the BDE group. Highest SFA was palmitic acid. Effective results were observed in the Bligh and Dyer applied groups in terms of both total lipid and total fatty acids. In cell disruption methods, particularly in enzyme and HCl extraction, good results were obtained in terms of fatty acids. The highest total fatty acids and the highest lipid content were detected in the Bligh and Dyer enzyme (BDE). Enzyme applications are also advantageous because of being environmentally friendly. Lipid health indices such as n-6/n-3, PUFA/SFA, Atherogenicity index (AI), Thrombogenicity index (TI) and hypocholesterolemic/hypercholesterolemic ratios (HH) were almost favorable. With this study, an appropriate lipid extraction methods were determined to provide an economical and environmental friendly suggestion for future studies to be used in areas such as food, feed and cosmetics.