The present invention relates to a separation membrane having both antibiotic and hydrophilic properties for water treatment and a preparation method thereof. In the separation membrane of the present invention, since an organic compound (antimicrobial and/or hydrophilic compound) is chemically conjugated to non-metal inorganic nanoparticles or metal nanoparticles, the nanoparticles are not eluted from the separation membrane even when the separation membrane is used for water treatment for a long period of time, so that the separation membrane may continuously maintain antimicrobial properties and high water permeability, is safe to the human body even when used for the treatment of drinking water, such as water purification, and exhibits characteristics in which stain resistance is also significantly enhanced due to antimicrobial and hydrophilic properties, which have been continuously imparted. Furthermore, high mechanical strength is exhibited by a metal or inorganic nanofiller introduced.