Refinement is usually used to remove undesired components to improve coconut oil quality. In the present study, crude coconut oil (CCO) was refined in four stages: conventional degumming, neutralization, bleaching, and deodorization. Physiochemical indices during the refinement were evaluated: peroxide value (PV), free fatty acid (FFA), fatty acid composition; fat composition; triacylglycerol profile, micronutrient (e.g., tocopherols and sterols) and contaminant (e.g., 3-monochloropropane-1,2-diol esters (3-MCPD esters), and glycidyl esters (GEs) levels. Compared to CCO, the quality of refined oil was improved by reducing PV and FFA levels. No significant changes in triacylglycerol compositions were found during refinement. However, unsaturated fatty acids like oleic and linoleic acids were decreased after refinement. Also, some micronutrients like tocopherol and sterol were decreased from 12.39 to 0.10 mg/kg and from 679.69 to 426.50 mg/kg, respectively. The undesired contaminants, i.e., 3-MCPD esters and GEs, increased markedly during refinement.