The invention relates to a design method of a deeply-buried PBA subway station section. The design method includes the following steps that a, a void is detected; b, a composite anchor rod pile (14) is driven on the ground; c, a large pipe shed (4) is applied; d, small pilot tunnels (2 and 3) are constructed; e, grille arch centers for the small pilot tunnels (2 and 3) are erected; f, initial supporting is conducted on the inner parts of the small pilot tunnels (2 and 3), and then side piles (5 and 6) are applied in the small pilot tunnels (2 and 3) correspondingly; g, a main body arch part (1) is excavated, initial supporting is conducted, and a secondary lining structure (9) is poured by concrete; h, a soil mass of a lower main body center (10) is excavated; i, a bottom plate (11), a side wall (12) and a middle plate (13) of a lower secondary lining structure of the lower main body center (10) are constructed; and j, an accessory structure is applied, and a complete station structureis formed. According to the method, the construction safety, the construction quality and the construction period can be ensured, the cost can be saved, and the construction efficiency can be improved; and section structure design is reasonable, the overall structure is stable, construction is easy and convenient, and the use effect is good.