The invention discloses a method for preparing carboxylated nanocellulose by hydrolyzing citric acid under a microwave condition. The method comprises the following steps: adding a bleached fiber pulpboard into a citric acid solution, hydrolyzing under a microwave condition, preparing cellulose nanocrystals through centrifugation, and preparing cellulose nanofibrils from residual long fibers through a high-pressure homogenizer. The method is green, non-toxic, short in consumed time, low in power consumption and relatively high in yield, and the used citric acid is easy to recycle, so that thepreparation cost of the nanocellulose is reduced, and engineering preparation of the nanocellulose is facilitated. Besides, the prepared cellulose nanocrystals and cellulose nanofibrils have relatively high dispersion stability, excellent specific surface area and relatively high carboxyl content, so that more chemical ways are provided for further modification of nanocellulose. Finally, the prepared nanocellulose has no residues of toxic and harmful substances, and has a wide application prospect in the aspect of functional materials taking cellulose as a substrate, especially in the aspectof materials related to human health.