The fast development of Internet of Things and MEMS/NEMS technologies has led the manufacture of chips and sensors towards micro/nano level, yet this poses huge challenges to dissipate heat in a limited space. Among various heat dissipation technologies, boiling heat transfer is a very promising method because of its rapid heat absorption caused by phase change. Though introducing different wettability to form a biphilic surface is recognized as a valid way to enhance boiling heat transfer, systematic and micro/nano scale investigations on the boiling process over patterned biphilic surface are still needed to meet the requirement of miniaturization. In this paper, a molecular dynamics study was adopted to investigate six biphilic surfaces with different hydrophilic/hydrophobic patterns. To the best of our knowledge, individual bubble behavior on biphilic surface was observed for the first time via molecular dynamics method. It was found that the bubble dynamics behaved differently when the wall temperature is 150 K and 200 K, respectively. In addition, the shape and volume of bubble could be controlled by designing the hydrophilic/hydrophobic patterns, and simulation results indicated that these patterns had significant effects on bubble inception temperature, film boiling temperature and evaporation rate. Also, an ever-present temperature and density difference were observed above biphilic surfaces, results shown that this difference helped to create a fluctuation and promoted horizontal heat and mass transfer, which in turn was considered to be favorable to bubble nucleation. In the end, different pattern designs were compared, results demonstrated that hydrophilic/hydrophobic pattern designing was important because heat transfer performance could be different even with the same hydrophilic to hydrophobic area ratio.