-Leadership The Japanese had great, and well disciplined Generals, why the Mongols were just "savages", and cared nothing; only about killing, and looting.
-Japanese Terrain Mongols were not used to mountainous terrains, they were horseman, and specialized in open field battle combat. The mountainous terrain of Japan made invading the Japanese one of the most difficult tasks for the Mongolians.
-Natural Disasters and "Typhoon Season" The Mongols couldn't have chosen a worse time to invade Japan. They invaded in the period known as "Typhoon Season". You see, most of the Mongolian ships were even lucky to return to home, because most of their ships sailed into hurricanes.
-Strong Morals While the Mongols had weak morality of fighting for just the sake of blood lust and loot, they were mentally weaker than the Japanese, who had strong morality over their independence, lives, their families, and their "homeland or motherland". This made the Japanese mentally more competent and capable than the Mongols.