Mannosylerythritol lipids (MELs), a glycolipid biosurfactant, possess great potential in many high‐value‐added fields. However, its water‐insolubility is an important obstacle to its wide application, especially in home and personal care fields. In this study, a new strategy “killing two birds with one stone” based on the chemical modification of natural MELs was developed for the preparation of hydrophilic MELs. These newly prepared MELs can be efficiently isolated from the reacted solution via stepwise extraction with a methanol/n‐hexane system. 88% of hydrophilic MELs were recovered from natural MELs, with a corresponding yield of 50%. This is mainly attributed to the esterification of fatty acids, representing the main and relatively‐difficult‐to‐remove impurities in fermentative‐produced MELs, facilitating separation from the MEL product via extraction. Moreover, these new MELs presented comparable surface activities to natural MELs while exhibiting enhanced water solubility and biocompatibility. This originates from the generation of MEL‐D, resulting from the deacetylation of natural MELs and the formation of new hydrophilic MELs containing just one hydrophobic chain (named “MEL‐G”). Hence, the present strategy is not only beneficial for the removal of impurities (fatty acids) but also for the preparation of MELs with improved hydrophilicity.