My father took his seat at the head of the table.

Literal

Father [topic-は] table's head-seat's own seat [at-に] sat-down.

上座 (かみざ) is the seat of honor — typically farthest from the door in a Japanese room or at the head of a Western-style table. 席に着く is a set expression meaning 'to take one's seat.' The concept of 上座/下座 (seating hierarchy) is fundamental to Japanese social etiquette.