Every morning I set my watch by the station clock.
Literal
Every-morning, station [possessive-の] clock [with-で] own [possessive-の] watch [object-を] align.
合わせる ('to match, to align') — here means 'to set' a watch. で marks the station clock as the instrument/reference used for the alignment. A charmingly old-fashioned habit in the age of smartphones.