The present invention relates to a mesenchymal stem cell having immunomodulatory activity and a preparation method therefor and, more specifically, to: a rapamycin-treated mesenchymal stem cell having immunomodulatory activity, which expresses any one or more cell surface factors selected from the group consisting of CCR1, CCR2, CCR3, CCR4, CCR7, CCR9 and CXCR4; a cell therapy composition comprising the mesenchymal stem cell, for preventing or treating immune disorders; and a preparation method for the mesenchymal stem cell having immunomodulatory activity. The rapamycin-treated mesenchymal stem cell having immunomodulatory activity, according to the present invention, has increased expression of IDO, TGF-β and IL-10 which are factors having immunomodulatory activity, has decreased expression of Phospho-mTOR, Rictor and Ractor which are signal transduction factors of mTOR, and has increased expression, in the cell, of autophagic inducer Beclin1, ATG5, ATG7, LC3I or LCII. If this cell is used as a cell therapy in individuals having immune disorders, it is possible to effectively treat immune disorders.