A common-mode (CM) suppression-based passive microwave measurement system for microfluidic applications is proposed in this article. The proposed system contains three parts, including differential microwave microstrip sensor, phase shifter, and power divider. The differential structure of the proposed microstrip sensor is composed of two split-ring resonator (SRR)-based microstrip sensors and four 3-D metallic walls. Interdigital capacitances (IDCs) are inserted between two SRRs to enhance the density of electric field. Moreover, two 3-D metallic walls are erected on both sides of each IDC, which can increase the concentration of electric field further. Power divider, phase shifter, and differential structure constitute the measurement system. Assuming that a signal with frequency of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${f}_{{0}}$ </tex-math></inline-formula> is input into input port, and going through by power divider, the CM signals will be generated. Then, passing by phase shift, differential structure, and combiner to output port, theoretically, when the phase difference between two branches is 180° at <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${f}_{{0}}$ </tex-math></inline-formula> , the corresponding magnitude of output signal will be zero at <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${f}_{{0}}$ </tex-math></inline-formula> . Therefore, the transmission coefficient will be infinitesimal at <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${f}_{{0}}$ </tex-math></inline-formula> (CM signals are suppressed), and an ultrahigh <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${Q}$ </tex-math></inline-formula> will be obtained. An equivalent circuit model is presented to reveal the operating principle of the sensor. The variations of relative frequency shift and normalized <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${Q}$ </tex-math></inline-formula> are adopted to extract the complex permittivity of liquid sample. In the experiment, the sensitivity of detecting real permittivity is about 0.05%, and a high <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${Q}$ </tex-math></inline-formula> of about 1432 is realized. All in all, the proposed microwave sensor has a huge superiority over some previously reported ones.