In this manuscript, a microwave sensing system for extracting complex permittivity of binary aqueous solutions based on a modified microstrip line with interdigital structure (IDS) etched is proposed. The passive resonance unit and active circuits constitute the microwave sensing system. The passive resonance unit is evolved from conventional microstrip line with the characteristic impedance of 50Ω, then the IDS is etched on the top surface of passive resonance unit to enhance the confinement of electrical field. The modified passive sensor can produce two resonant modes, i.e., odd-mode 1 and odd-mode 2, the electrical fields of these two modes are both concentrating at IDS, and odd-mode 1 with higher density of electrical field is adopted to retrieve complex permittivity of liquid samples. Except for the passive sensor, the sensing system consists of power divider, low noise amplifier (LNA), isolator, orthogonal hybrid coupler, phase shifter, mixer, and low-pass filter (LPF). The proposed microwave sensing system has two output DC voltages, i.e., channel-I and channel-Q. The mathematical relationship between complex permittivity and resonant frequency shift can be transformed into the relation between complex permittivity and two DC voltages by the proposed microwave sensing system, which is beneficial to discard the use of VNA. The two output voltages of microwave sensing system will be changed according to the injections of liquid samples with different complex permittivity, then the mathematical models can be established by summarizing the rule between complex permittivity and DC voltages. Finally, the established mathematical models can be adopted to predict the binary aqueous solutions with unknown complex permittivity. In measurement, the proposed microwave sensing system has the average sensitivities of about 2.478 mV/εr′ and 1.418 mV/εr′ for channel-I and channel-Q, respectively, which are several times higher than other reported ones. Low-cost, high sensitivity, convenient measurement, and easy fabrication are the merits for the proposed sensing system, and it is a good template in the region of detecting liquid samples.