Mortierella alpina, an oleaginous fungus, has been shown to be a potential source for arachidonic acid (ARA) production. The recovery of intracellular lipids from M. alpina is an important step for the downstream bioprocessing, and green extraction techniques with a focus on being efficient and eco-friendly have drawn much attention. In this study, different cell disruption techniques (mechanical: high-speed homogenization 10,000 rpm, ultrasonication 20 kHz, high-pressure process (HPP) 200–600 MPa; non- mechanical: acid treatment HCl) were investigated for lipid recovery from M. alpina, and process parameters (A. temperature, B. pressure, C. cosolvent ratio) of supercritical carbon dioxide (SC-CO2) lipid extraction were studied by applying response surface methodology (RSM). Compared with Soxhlet extraction as a control group (100%), high-speed homogenization has the highest lipid recovery (115.40%) among mechanical disruption techniques. Besides, there was no significant difference between high-speed homogenization and 1 M HCl treatment (115.55%) in lipid recovery. However, lipid recovery decreased to 107.36% as the concentration of acid was increased to 3 M, and acid treatment showed a negative effect on the ARA ratio. In HPP treatment, the highest lipid recovery (104.81%) was obtained at 400 MPa, 1 time of treatment and water medium. In the response surface model of SC-CO2 extraction, results showed the major influence of the process parameters to lipid recovery was pressure, and there are interaction effects of AC (temperature and cosolvent ratio) and BC (pressure and cosolvent ratio). Lipid recovery of SC-CO2 extraction reached 92.86% at 201 bar, 58.9 °C and cosolvent ratio 1:15. The microbial lipid recovery process of this study could be used as a reference and an eco-friendly alternative for the future downstream bioprocessing of ARA production by M. alpina.