Godzilla: King of the Monsters’ Ghidorah would probably be the winner of a hypothetical showdown with Kong. Since Godzilla soundly defeated both of them, there’s no question who the MonsterVerse’s most powerful Titan is, but as for who the second strongest is, that’s not entirely clear. Kong was only a third of Godzilla’s size in Kong: Skull Island, but the MonsterVerse elevated him to a record-breaking new height by making him over 360 feet tall for its fourth adventure.
In Godzilla vs. Kong, Kong was depicted as a rival alpha to Godzilla and the only active Titan who could be regarded as a threat to Gojira’s reign. Plus, it was revealed that his species shared an ancient rivalry with Godzilla’s kind that stretched back thousands of years. It was renewed in the movie when Monarch and APEX moved Kong off Skull Island and into Godzilla’s crosshairs. The two Titans engaged in three epic clashes that ended with Godzilla proving his dominance.
Kong succeeded in really pushing Godzilla at certain points, which showed that he is truly is a worthy opponent to the King of the Monsters. However, that doesn’t necessarily mean he’s the greatest foe Godzilla has ever faced. That title could belong to Ghidorah instead. It’s worth wondering what would have happened if Kong – rather than purposely ignore Ghidorah’s call – had answered it with a challenge. A line in the movie suggests Kong would have lost such a fight. When Monarch was deciding what to do about the monster, Colonel Foster asked if there was another Titan who might stand a chance against him. Serizawa responded by saying only Godzilla could beat him.
As Monarch’s leading Titan expert, Serizawa had access to all sorts of information on the MonsterVerse’s Titans. At the time, they had files on seventeen of these monsters, Kong included. If any of them had the physical capabilities to contend with Ghidorah, it makes sense that Serizawa would know that and have mentioned them. The fact he didn’t bring up Kong at all is telling.
How would a fight between them have turned out? Against Ghidorah, Kong would have faced three problems: Ghidorah’s three heads, his regeneration powers, and his gravity beams. Kong, who had to have help from one of APEX’s HEAVs to beat a Warbat, would have struggled mightily against all of Ghidorah’s offensive weapons. Kong, who lacks the raw power and impressive durability of Godzilla, would have had a harder time holding off all three heads trying to attack him at the same time. The gravity beams would have done significant damage as well, especially since it’s known from Godzilla vs. Kong that Kong is weak to "flammable attacks".
For the most part, he managed to avoid Godzilla’s atomic breath, but that would be a lot more difficult with Ghidorah, since he has three heads to blast him with. If Kong had the axe, there’s a chance he’d put up a good fight and may have cut off a head at the most, but the Godzilla: King of the Monsters villain would still hold the advantage in terms of power. If he did need some distance, he could fly away and bombard Kong with gravity beams (which the Titan would have no answer for). Ghidorah, who came closer to killing Godzilla than Kong ever did, likely would have defeated the giant ape.