From Halopedia, the Halo wiki
EC# (presumed to be short for Enemy Combatant Number) is a form of identification used by the UNSC when noting individual enemy combatants that have participated in various battles against the UNSC. The system is used primarily to identify Covenant warriors. Each individual warrior gets its own number, which consists of a letter (signifying the combatant's race) as well as two sets of three digit numbers. It is unclear how long the UNSC has been using this system, other than that it was in use as early as 2552, and several combatants were identified during the Battle for Earth, such as Sangheili and Unggoy.