We employ the Feedback In Realistic Environments (FIRE-2) physics model to study how the properties of giant molecular clouds (GMCs) evolve during galaxy mergers. Due to the rarity of mergers in the local Universe, samples of nearby merging galaxies suitable for studies of individual GMCs are limited. Idealized simulations provide us with a new window to study GMC evolution during a merger, and assist in interpreting observations. We conduct a pixel-by-pixel analysis of the simulated molecular gas properties in both undisturbed control galaxies and galaxy mergers. The simulated GMC-pixels follow a similar trend in a diagram of velocity dispersion (σv) versus gas surface density (Σmol) as observed in normal spiral galaxies in the Physics at High Angular resolution in Nearby GalaxieS (PHANGS) survey. For simulated mergers, we see a significant increase in both the Σmol and σv for GMC-pixels by a factor of 5 – 10, which put these pixels to be above the trend of PHANGS galaxies in the σv vs Σmol diagram. This deviation indicates that GMCs in the simulated merger are more gravitationally unbound and have higher virial parameter (αvir) of 10 – 100, which is much larger than that of simulated control galaxies. Furthermore, we find that the increase in αvir generally happens at the same time as the increase in global star formation rate (SFR), which suggests feedback is playing a role in dispersing the gas. The correspondence between high αvir and SFR also suggests some other physical mechanisms besides self-gravity are helping the GMCs in starburst mergers to collapse and form stars.