Fluid-elastic instability (FEI) is the most dangerous vibration mechanism in tube arrays. As the research shows in the recent years, the mechanism of FEI turns to be clear, but threshold prediction in low mass damping parameter (MDP) tube arrays is still not accurate because of the complexity of the instability mechanism. In this work, computational fluid dynamics (CFD) simulation is first validated by comparison with the water tunnel experiments in four kinds of tube arrangements and then extended to two-phase flow to get more data in low MDP range. Using fluid force coefficients calculated by CFD simulation, unsteady modeling of the tube model is established and the critical velocities match well with experiment and CFD simulation results. The effect of tube arrangement and Reynolds number on the fluid force coefficients and the predicted critical velocity is studied according to the unsteady flow theory. The results show that instability critical velocity of the normal triangular array can be underestimated at MDP lower than 1. When the frequency ratio (streamwise direction to transverse direction) decreases to below 0.8 in the rotated triangular array, the streamwise instability occurs earlier than transverse instability. The methods and conclusions in this paper can be used in FEI analysis in both streamwise direction and transverse direction.