The JEM elements are delivered to the ISS on three Shuttle flights and are assembled on orbit subsequently. The verification of JEM structural compatibility with the Space Shuttle was performed to certify its flight readiness. Structural compatibilities are required on weight and center of gravity, stiffness and structural damping, strength, and dynamic clearance. Verification results should be reviewed at several assessment stages and needs to be approved by NASA for flight certification. On the other hand, JEM is the Japanese first manned-base facility, and has complicated interface with the Space Shuttle. So several issues were found in the verification phase and have been successfully resolved by technical challenges on Lack of Ascent Performance Margin (APM), Non-linear stiffness of structural latch mechanism, Negative structural margin, and Close clearance / Interference.