Recently, edible oil has been employed for biodiesel feedstocks. However, the use of such oil to fulfil energy demand raises certain problems, such as the sustainability of the practice due to its competition with food. Therefore, it is necessary to obtain alternative resources from non-edible oil. One promising biodiesel feedstock from a non-edible oil source is crude Calophyllum inophyllum oil (CCIO) because of its high oil content. The highest oil content in CCIO is triglyceride (TG), which influences biodiesel production. The higher content of TG results in a higher yield of biodiesel. Previous research on the conversion of CCIO into biodiesel with an environmentally friendly purification method and fast separation of compounds is limited. In this work, batchwise solvent extraction (BSE) and microwave-assisted extraction (MAE) were compared to achieve an effective and efficient method for TG purification. By using the microwave method with 450 watts of power for 30 minutes, a high content of TG was obtained. It was found that TG content increased significantly, from 75.99% to 83.46%. Using the BSE method with a mixture of petroleum ether−methanol (methanol 25%), a solvent-to-oil mass ratio of 5:1, time for the first 2 stages (48 hours), the TG content obtained was 82.02%. The data obtained for the microwave method are almost equivalent to the first 2 stages of BSE with regard to TG content (83.46% compared to 82.02%) and almost 0.01 times shorter than BSE (30 minutes compared to 48 hours).