All above-ground train services will be suspended when a No 9 typhoon signal or higher is hoisted, the MTR Corporation said.
Miranda Leung Chan Che-ming, MTR Corp's corporate relations general manager, said the decision came after the railway registered complaints from hundreds of passengers stranded in stations when Typhoon Vicente hit the city in July.
She said services will be stopped at all stations along the East Rail, Ma On Shan, Tung Chung, Disneyland Resort and Airport Express lines under the No 9 typhoon signal or higher.
Some stretches of the Tsuen Wan, Kwun Tong, Island and West Rail lines, the Light Rail and MTR buses will also cease service.
Richard Tsoi Yiu-cheong, of the Coalition to Monitor Public Transport and Utilities, said the MTR's new arrangement was unnecessary and would inconvenience many passengers.