Time Crisis 3 incorporates a new type of weapons system allowing the player to switch between the standard 9-round handgun, a fully automatic machine gun that can hold 200 rounds, a shotgun with 50 rounds and a 5-round grenade launcher with powerful splash damage. Only the handgun has unlimited ammunition, though players can shoot yellow-clad soldiers to gain ammunition for their other weapons.

The game incorporates a new type of weapons system allowing the player to switch between the standard Smith & Wesson SW99 9-round handgun, a fully automatic Ingram MAC-11 machine gun that can hold 200 rounds, a Remington 870 shotgun with 50 rounds, and a Leuchtpistole 5-round grenade launcher with powerful splash damage. Like its predecessor, it retains the no-miss combo. Hence, the center shot from the shotgun must hit a target to maintain the no-miss combo and the grenade resets it. Also, maximum amount of points earned via time bonus per area is capped at 99,990 points.