In this paper, flexible substrate integrated waveguide (SIW) resonators have been designed and fabricated on polyimide substrates for humidity sensing applications. The proposed SIW resonant cavity allows the resonator to obtain the maximum humidity sensitivity and meet the demand for flexible microwave sensing detection. Meanwhile, the humidity response performance can be further significantly enhanced by introducing nanodiamond (ND) sensing material. Three prototypes of ND-coated SIW sensors with different bending radii are measured to analyze their humidity sensing performance. The experimental results demonstrate that the proposed ND-coated SIW sensor with the minimum bending radius can achieve a maximum humidity sensitivity of 1.09 MHz/% relative humidity (RH) in the high RH region (>75.3% RH) and a low humidity hysteresis of 1.8% in the range of 11.3–97.3% RH. This study provides a promising candidate to realize flexible microwave sensors with excellent sensing performance.