The company where my father works is near the station.
Literal
Father [possessive-の] is-working company [topic-は] station's nearby [at-に] exists [polite-ます].
父の働いている会社 is a relative clause: 'the company at which father is working.' The の after 父 can replace が inside a relative clause — a common pattern that sounds more natural than 父が働いている会社 in this context.