Efficient cost effective lipid extraction from microalgae is a challenging topic for large scale production of microalgae-based biodiesel. In this study, a microwave-assisted lipid extraction process was applied to the oil-rich green microalga Scenedesmus obliquus grown on municipal wastewater. N-hexane/isopropanol solvent was used as alternative solvent. Optimal extraction parameters were determined as: operational temperature of 130 °C, extraction time of 0.25 h, solvent ratio of N-hexane/isopropanol of 3:2 (V:V), phase ratio of co-solvent/biomass was 50:1 (mL:g). Relative extraction rates of lipid and fatty acid methyl esters (FAMEs) achieved using microwave-assisted extraction (MAE) were 88.25% and 95.58%, respectively, which is higher than traditional water bath heating extraction process (WHE). In addition, compared with WHE, the apparent first order rate constant of MAE was enhanced by 18 times compared to traditional methods. Analysis using scanning electron microscopy indicated that disruption of the cell wall of Scenedesmus obliquus by microwave led to the enhancement of solvents’ penetration and lipid extraction.