Fatigue failure of solder joints is a serious reliability concern in area array technologies. A non-linear finite element model was made to study the effects of underfill material and substrate flexibility on solder joint thermal fatigue. Accelerated temperature cycling loading was imposed to evaluate the reliability of solder joints in test flip chip assembly. The results show that the underfill material and substrate flexibility can improve the distribution of stress/strain and reduce the magnitude of stress/strain in the solder joints. Therefore, the reliability of solder joints under thermal cycling condition can be enhanced by applying underfill material and selecting the Flex substrates during temperature cycling.