After throwing one of the Omuai, he will bounce three times, and you need to hit him four. So, try to hit it every time when he comes down, and if you miss once, do a spin attack after he lands the last time.
In the beginning of the fight, there's a pause before you can hit him, so charge up a spin attack. While Mothula is flying around, stand in a corner and charge spin attacks. When he goes in the middle, he will begin charging up either a fire ball attack or send out moths. Slash him as he is charging up, then jump as soon as he sends out the fireballs or moths to avoid being knocked into the holes.