Players can use Link Disc feature with DJMax Portable Clazziquai Edition, allowing them to play the songs of Clazziquai Edition along with song patterns and RD patterns unique to Black Square. The RD songs can also be listened to on a special disc in Album Mode. This pattern is a remixed version of the song, and is usually harder. Some songs have a special pattern, called RD style, that appears in the place of MX patterns on the song selection screen. Black Square introduces RD (Redesign) song patterns to the game series.

The music starts playing again when the next special note is hit, and the extra points are reset to 1000. The note also has a penalty - the music stops if it is missed.

In Black Square, a specialized note appears that's a different color than the rest, hitting these notes gives the player 1,000 bonus points and 1,000 extra points every time they hit another note of the same kind (ex: hit once in a row: 1,000, hit twice in a row, 2,000, hit ten times in a row: 10,000). Black Square also has an extended Club Tour mode. Black Square has an enhanced Fever bonus which can go up to a x7 multiplier. Black Square features note auto-correction which corrects the notes player misses.

8B Mode has been re-introduced into the series and has been renamed 6BFX Mode for this release. In Black Square, 2B Mode, which was featured in Clazziquai Edition, has been removed.

It has the same user interface as Clazziquai Edition, but with a different 'Bling Style' theme. DJMax Black Square features largely the same features as Clazziquai Edition, but with increased difficulty and an almost completely different song list.

Ppssp djmax portable 3 setting