The heat generated during the bearing working process would greatly affect the working life and stability of bearing and mechanical transmission system. To analyze the heat generation of cylindrical roller bearings (CRBs), a theoretical calculation model of bearing friction torques is proposed. The differences in friction torque between the flexible and rigid CRBs are compared. The waviness error on the rings and rollers is considered. To study the bearing transient temperature characteristics, a thermal network is established, and the transient heat balance equations are solved. An optimization algorithm for manufacturing parameters of a CRB with the low friction torque is conducted, in which the waviness error is considered. The results show that the radial force, speed, and waviness can greatly affect the friction torque and temperature characteristics of CRB. The friction torque and outer ring temperature increase with the increment of radial force, speed, and waviness amplitude and order. The friction torque and temperature of CRB can be effectively reduced by changing the bearing manufacturing parameters. This study can provide some guidance to the optimal design method of CRB with the low friction torque.