Pollutants, such as black powder, are commonly found in natural gas pipelines and are considered undesirable. These pollutants not only degrade the quality of natural gas, but also contaminate compressor components and can even corrode and damage the pipeline, leading to serious safety hazards such as pipeline blockages. This paper proposes and investigates a novel circular probe microwave resonance sensor (CPMRS) to dynamically measure pollutants in natural gas pipelines at an early stage. The influence of the circular probe structure on the CPMRS performance and the optimal structural parameters of the CPMRS are studied using finite element simulation software. An experimental platform is then set up to evaluate the resonance of the CPMRS in different working conditions. The results show that the resonance frequency shift can reach up to 4.27 MHz for the mass flow rate of 12.54–78.69 mg/s. Additionally, the results demonstrate that the magnitude of the phase change of CPMRS is considerably greater than the magnitude of the amplitude change. The results also indicate that CPMRS is more sensitive to pollutants and more resistant to flow velocity perturbation than ordinary transmission probe microwave sensors.