Terahertz (THz) waves have garnered significant interest across various fields, particularly in high-sensitivity sensing applications. Metamaterials can be employed in THz sensors, specifically for refractive index sensing and pesticide detection due to their high-sensitivity characteristics. In this Article, a dual-band flexible THz metamaterial sensor based on polyimide is proposed for refractive index and pesticide sensing, which is fabricated using ultraviolet (UV) lithography technology and measured by a THz time-domain spectroscope (TDS) system. The resonant frequencies of the sensor are at 0.37 and 1.13 THz, with transmission rates of 2.9% and 0.3%, respectively. With an analyte layer attached to the sensor's surface, the sensitivity of refractive index sensing can be calculated as 0.09 and 0.28 THz/RIU (refractive index unit) at the two resonant frequencies. In order to validate the exceptional pesticide sensing performance of the sensor, chlorpyrifos-methyl acetone solutions with various concentrations are added on it. Furthermore, a monolayer of graphene is coated on the sensor's surface, which is proved capable of improving pesticide sensing sensitivity at low concentrations due to strong π–π stacking interactions with π-electrons in chlorpyrifos-methyl solutions. Therefore, the graphene-coated sensor can be utilized in detecting pesticide solutions with low concentrations, and the sensor without graphene is preferred for high concentration detection. This work provides a novel option for the THz metamaterial sensor with high sensitivity covering a wide pesticide concentration range.