In order to study the heat conduction, convection and heat flux density of blood for blood pump rotor system,and established the three-dimensional model of the blood pump rotor system in Solidworks, and then will establish a model to lead the finite element analysis in ANSYS Workbench, thermal analysis, the result of analysis is temperature distribution and heat flux distribution and temperature deformation figure of the blood pump rotor system. Through the study, the rise of temperature of the blood pump rotor system meets the requirements, and The structure design is reasonable;the blood pump rotor system overall deformation is small,but it’s not affect the normal work of the blood pump, It could provided data to support the optimization design of the blood pump rotor system.