Some demonstrators were seen smashing CCTV cameras, Octopus card machines and destroying some glass panels.
They also dug up bricks from the area and threw iron bars and large rocks on to the tracks. Roadblocks were also push up around the station.
MTR said light rail lines 507, 614P and 615P were suspended due to the damages. Other lines will also be diverted to avoid the Tuen Mun area.
Meanwhile, the rail operator had shut the Tuen Mun west rail station two hours before the police-approved rally was to start. This has angered many residents who had to find other ways to move around during the weekend.
The protesters have also accused MTR of not providing service for the public and only helping police officers.