Besides normal rebalancing from Continuum Shift Extend, Chrono Phantasma features several revamped gameplay mechanics and introduces seven new characters to the roster (with two additional characters added to the Extend version of Chrono Phantasma). The character sprites have also been redrawn and several new songs were composed for the game. All previous musical themes were re-arranged. The storyline continues after events of Continuum Shift.

A new mechanic called "Overdrive" has been added to the game, replacing the Gold Bursts from Continuum Shift. Green Bursts are still in but are the only form of Burst available. Distortion Drives such as Ragna's "Blood Kain", Taokaka's "Almost Becoming Two!", Litchi's "Great Wheel" and Bang's "Fu-Rin-Ka-Zan" have been retooled to be their respective characters' Overdrives. The length of an Overdrive increases the lower a character's health is, and performing an Overdrive stops the round timer while it is active.

Guard Primers have been removed entirely and the Guard Crush has been moved to a new mechanic called "Crush Trigger" where, at the cost of 25 Heat, a player may hit the A and B attack buttons simultaneously to cause a Guard Crush against blocking opponents, provided the opponent is not using Barrier Block.