A method for producing induced pluripotent stem cells by using CRISPR/Cas system is disclosed. The method includes a step of inserting a reprogramming factor by using a CRSPR/Cas system containing in a safe harbor of somatic cells a delivery means including two guides RNAs and a Cas protein-encoding nucleic acid. The method can prevent mutation in an off-target region and integrate a reprogramming factor into an on-target region safely and specifically, and regulates the reprogramming factor with doxycycline to guarantee consistent expression, whereby induced pluripotent stem cells can be effectively produced. In addition, the induced pluripotent stem cells produced by the method exhibit multipotent markers similar to those of human embryonic stem cells and can differentiate into derivatives of all the three germ layers.