In the flow-induced vibration analysis of the heat exchanger tube of the stream generator, the damping of each position on the tube is different, since the secondary side of the tube is the two-phase flow (stream-water) and the void-fraction is gradually increased from bottom to top. It is necessary to study the simulation of the tube damping in non-uniform two-phase flow. The study is based on the Pettigrew's damping formula of tube in two-phase flow and the void-fraction distribution along the tube in the typical example. For the two-phase damping component of the tube damping, the disadvantage of damping overestimation of void-fraction processing method in common engineering software are analyzed. The reason is the nonlinearity of the void-fraction influence coefficient. The method of segmentation weighting void-fraction is developed. The effects of different segment lengths are studied, indicating that the section lengths should be minimized. For the subsequent segmentation damping weighting problem, the effects of different weighting factors in engineering methods and standards are compared, and the difference is small. The results of flow-induced vibration analysis with different damping inputs were compared to judge the applicability of Pettigrew's damping formula. From the above four researches, the recommended simulation method of the tube damping in non-uniform two-phase flow is given to more accurately carry out the flow-induced vibration analysis of heat exchanger tube.