To solve the problem of the limited sensitivity， which is due to the poor interaction between the analytes and the localized enhanced electromagnetic field， the terahertz microfluidic sensor based on a metamaterial absorber with the enhanced electromagnetic field interaction is proposed by introducing the microfluidics technology. Owing to the interaction of the sensor and terahertz waves， the magnetic dipole resonances are excited and two significant absorption peaks with the absorption rates over 98% are formed in the range of 0.4~1.4 THz. Meanwhile， with integrating the microfluidic channel， the interaction between the analytes and the localized enhanced electromagnetic field located in the Fabry-Pérot cavity is dramatically enhanced， and the sensor can reach the high sensitivity of 537 GHz/RIU. In addition， the unit cell is designed as the four-fold rotational symmetrical structure， so that the polarization-insensitivitive and the wide range of incident-angle-insensitive properties of the sensor are obtained. The results indicate that the proposed sensor has the characteristics of high sensitivity and polarization-independent， and it exhibits a promising application prospect in the field of label-free trace detection.