In this paper, high quality seismic data in 1964~2003 from the ISC (International Seismological Centre) catalog are used to present a relatively more complete and definite geometric structure of the intermediate seismic zone in the Pamir‐Hindu Kush region. Dip directions and the largest depth of the Hindu Kush intermediate seismic zone (H zone) and the Pamir intermediate seismic zone (P zone) change along the strike, so they can be further divided into five segments: HW (west segment of the H zone), HE (east segment of the H zone), PSW (southwest segment of the P zone), PM (middle segment of the P zone), and PNE (northeast segment of the P zone). There is a seismic gap in the H zone at about 170~190 km depth, beneath which the seismic zone dips nearly vertically. Meanwhile, the seismic zone beneath the gap forms an inverted V‐shape zone, the two branches of which are nearly perpendicular with each other. The west branch within the HW segment does not have double seismic layers. The east branch within the HE segment is deeper and has double seismic layers. Focal mechanism solutions of the intermediate earthquakes have regular patterns. In the Hindu Kush region, most T axes are nearly vertical while most P axes are nearly horizontal and perpendicular to the strike of the seismic zone. In the Pamir region, from southwest to northeast, horizontal along‐strike axis changes from P to B and then T; P axes gradually change to be perpendicular to the strike. At last, we discuss the possible geodynamic explanations for the seismicity in this region.