Nam Cheong station was originally the western terminus of the West Rail line before the opening of Kowloon Southern Link on 16 August 2009.

[2] The station was opened for public use on 16 December 2003, coinciding with the pre-opening charity trial run day of the KCR West Rail (later West Rail line), and the Tung Chung line part of the station started operation.

The operations of MTR and KCR merged on 2 December 2007, and the management of the station unified under MTRCL.

One of the wider passages is aligned with the fifth and sixth carriages of the Hong Kong-bound trains on the Tung Chung line platform.

Hence, Nam Cheong was included in the project and is now an intermediate station on the Tuen Ma line.

Before the merging of fare systems on 28 September 2008, Octopus card users transferring between the West Rail line and Tung Chung line had to use the transfer gates separating fare areas the MTR and KCR systems.