We report an ion-scale magnetic flux rope (the size of the flux rope is similar to 8.5 ion inertial lengths) at the trailing edge of Kelvin-Helmholtz (KH) waves observed by the Magnetospheric Multiscale (MMS) mission on 27 September 2016, which is likely generated by multiple X-line reconnection. The currents of this flux rope are highly filamentary: in the central flux rope, the current flows are mainly parallel to the magnetic field, supporting a local magnetic field increase at about 7 nT, while at the edges the current filaments are predominantly along the antiparallel direction, which induce an opposing field that causes a significant magnetic depression along the axis direction (> 20 nT), meaning the overall magnetic field of this flux rope is depressed compared to the ambient magnetic field. Thus, this flux rope, accompanied by the plasma thermal pressure enhancement in the center, is referred to as a crater type. Intense lower hybrid drift waves (LHDWs) are found at the magnetospheric edge of the flux rope, and the wave potential is estimated to be similar to 17% of the electron temperature. Though LHDWs may be stabilized by the mechanism of electron resonance broadening, these waves could still effectively enable diffusive electron transports in the cross-field direction, corresponding to a local density dip. This indicates LHDWs could play important roles in the evolution of crater flux ropes.