Embryonic stem (ES) cells are well known for their differantiative totipotency and expected promising materials for the next generational regenerative medicine. But the differantiative mechanism of ES cells has been unexplained. The purpose of this study is to prepare a new ES cell culture system, which can maintain ES cells undifferentiated state by controlling ES cell colony size. For this purpose, we design noncytotoxic, cell-adhesion controllable and easily pattern formable polymer material. In this study, we prepared the micro-pattern surface by using with photo-reactive phospholipid polymer to regulate the growing scale of ES cells. This photo-reactive polymer was synthesized by a coupling reaction involving copolymer consisting of 2-methacryloyloxyethyl phosphorylcholine and methacrylic acid with 4-azidoaniline. We cultured mouse ES cells (129/Sv) on cell adhesion selective micro-patterned well made of photo-reactive phospholipid polymer. By alkaline phosphatase staining analysis against confluent ES cells in each well, ES cells cultured in micro-patterned well dyed much better than normal TCPS-cultured ES cells. This result indicated that the colony size of ES cells related to their differentiation state. We could control differentiation function of ES cells by controlling cell culture area in micro order..