Following along from the Hanagumi Taisen Columns 2 , the game features a few refinements to the gameplay formula. The biggest change is the introduction of a battle mode selection system, allowing the player to choose one of four different styles to alter their character's gameplay. Forest is a balanced style which behaves like the rules of the previous game, with the player able to store up to three levels of super meter; Wind limits the player to only two levels of meter, but fills the meter more quickly; Mountain starts the player off with additional meter at the penalty of filling meter more slowly; and Fire allows the player to fill their meter to 4 but limits the maximum level of defensive attack to 2. Two additional modes are unlockable after completing certain story modes: Shadow, which starts with the player's meter completely full but with a major penalty to refilling it; and Lightning, which allows the player to fill their attack meter to 4 and grants a major boost to the speed at which they fill it, but prevents the player from using any defensive options at all.
The visual novel story mode follows a similar plot to the first game, but this time focuses on a production of Shonen Red vs. Benitokage with the characters competing for the role of Shonen Red. An extra unlockable story mode becomes available once the player has unlocked the four secret characters and focuses on them specifically.
The gameplay is primarily focused on clearing levels using different combinations of columns to create line sequences that match or exceed a target number. Points are awarded for each successful sequence, with higher scores awarded for longer sequences and more complex combinations. The game also features a time attack mode, where the player must clear as many levels as possible within a set time limit.