The disclosure provides a penetrating high wing structure of civil aircraft with blended-wing-body, wherein the structure comprises a left wing, a right wing and a high wing penetrating central wing. The left wing and the right wing are symmetrically arranged and connected to two sides of the high wing penetrating central wing through fasteners respectively, and the high wing penetrating central wing is arranged on the top of the main body. The left wing and the right wing both comprise wing ribs and wing spars that are arranged in a crisscross way. The disclosure proposes a penetrating high wing structure, wherein the wing and the body are designed as a whole so that the wings will not damage the continuity of the internal space of the body, which improves the load transfer efficiency of the structure and reduces the fasteners used for connection, thus reducing the weight of the body.