TwinBee can be played by up to 2-players simultaneously. The player takes control of a cartoon-like anthropomorphic spacecraft, with Player 1 taking control of TwinBee, the titular ship, while Player 2 controls WinBee. The game controls consists of an eight-way joystick and two buttons: one for shooting enemies in the air and the other for dropping bombs to ground enemies (similarly to Xevious).

The player’s primary power-ups are bells that can be uncovered by shooting at the floating clouds where they’re hidden. If the player continues shooting the bell after it appears, it will change into one of four other colors: the regular yellow bells only grant bonus points, the white bell will upgrade the player’s gun into a twin cannon, the blue bell increases the player’s speed (for up to five speed levels), the green bell will allow the player to create image copies of its ship for additional firepower, and the red bell will provide the player’s ship a barrier that allows it to sustain more damage. The green and red bells cannot be combined together. Other power-ups can also be retrieved from ground enemies such as an alternate bell that gives the player’s ship a three-way gun, a star which eliminates all on-screen enemies.

As with other games of the same genre, getting shot by a single enemy bullet will cause the player to lose a life. However, if the bullet only strikes either side of the ship instead, the player’s ship will only lose one of its arms. If the player’s ship loses both arms, it will lose the ability to throw bombs and the player must wait for an ambulance to arrive. The player must navigate their ship to the ambulance to repair their arms. However, if the player’s ship loses both arms for the second time, no ambulance will arrive.

If two players are playing at the same time, they can align their ships vertically or horizontally together to perform more powerful attacks