Abstract: Aiming at the limitation of detection ability of VHF coherent scattering radar in routine mode, a detection system based on interference method is constructed to form the detection ability of three-dimensional fine structure of ionospheric E region field-aligned irregularity (FAI) in this work. Based on E region FAI echo data obtained by VHF radar interference detection experiment carried out at Qujing, the phase deviation of detection system is calibrated and the three-dimensional fine structure and drift motion process of E region FAI are obtained. It includes the three-dimensional position of the FAI echo scattering point and the three-dimensional outer scale of the FAI cloud cluster, drifting trajectory and drifting velocity, etc. Observed results show that the east-west, north-south and altitude ranges of E region FAI structure are within −35−20 km, 85−120 km and 95−130 km, respectively, and the corresponding three-dimensional outer scales are 23.8 km, 7.6 km, and 7.6 km, respectively. The drift velocity in the east-west direction is greater than that in other directions. Quasi-periodic echoes with the period of 5−6 min are also presented in this study. It completely and accurately reveals the spatiotemporal evolution process of FAI in the E region from generation to disappearance.