A multiple resonance peaks terahertz metamaterial sensor based on double-cross structure was designed. The overall structure was composed of surface metal pattern, intermediate medium and bottom metal plate. The surface pattern of the basic unit was double-cross and the medium material was polyimide. The simulation results show that the proposed structure has five different resonant absorption peaks, and the absorption rate is more than 90%. The first three resonance peaks correspond to the basic magnetic resonance formed in different regions of the unit structure, and the last two resonance peaks are derived from the interaction between the unit structures. When the surface of the sensor is covered with an analyte with a thickness of 15μm, the sensitivity of each resonance peak of the sensor is 72, 137, 234, 353 and 252GHz/RIU, respectively. The resonance peak offset has a strong linear relationship with the refractive index change of the analyte to be measured, which has superior sensing characteristics. In addition, the stability of the multiple peaks sensor is better than that of the traditional single peak or double peak sensor, which has good anti-interference ability to reduce the measurement error. The proposed high sensitivity multiple resonance peaks sensor has a broad application prospect in the field of trace molecule detection.