A novel dual band, highly sensitive Substrate Integrated Waveguide (SIW) sensor for permittivity measurements is presented. A pair of modified Complementary Split Ring Resonators (CSRRs) is etched on SIW surface. CSRRs are located in the center of SIW, where the electric field distribution is high so that the coupling be maximized. The coupling between the SIW and the CSRRs as well as the adjacent CSRRs results in two notches in transmission coefficient. These notches vary with the dielectric loading on the sensor. The ratio of a notch variation to the load permittivity variation determines the sensitivity of proposed sensor. Two sensitivities proportional to two notches are provided. Normalized sensitivities from both notches show identical values. Therefore, any environmental effect have the same variation on the TZs. This demonstrates the potential of the proposed sensor for differential operation that can mitigate the effect of environmental condition. The size of the proposed sensor is small as the inductive and the capacitive effects of CSRRs forced the SIW to operate below the cut off frequency at negative-order-resonance mode. All design steps including SIW design, CSRRs design and modified CSRRs effects are presented in details. The sensor operation principle is described through an equivalent circuit model as well as simulation results. The experimental results indicates that the normalized sensitivity is 3.4% which is much higher than similar sensors. The prototype sensor size (27.8 x 18.4 x 0.508 mm(3)) is smaller than those reported in the literature.