The present invention relates to a method for preparing differentiated cells derived from induced pluripotent stem cell, wherein undifferentiated induced pluripotent stem cells (iPS) are removed, the method comprising steps of: (a) preparing a cell sample including undifferentiated induced pluripotent stem cells and differentiated cells by differentiating induced pluripotent stem cells; and (b) causing selective apoptosis of the undifferentiated induced pluripotent stem cells by treating the resultant in step (a) with quercetin of Formula 1 below or with YM-155 of Formula 2 below.According to the present invention, the present invention makes it possible to effectively selectively cause apoptosis only of undifferentiated induced pluripotent stem cells by causing induced pluripotent stem cells to differentiate into specific differentiated cells and then carrying out culturing in a differentiating culture medium comprising quercetin or YM-155, and, in the induced pluripotent stem cell differentiation method according to the present invention, only undifferentiated induced pluripotent stem cells that are a cause of teratoma formation are selectively caused to die, and thus differentiated differentiating cells are completely unaffected. In other words, the invention can be expected to ensure safety as the possibility of tumor formation during clinical use as a cell therapeutic agent is eliminated since the survival and functioning of the differentiated cells is maintained unchanged.