Microwave sensors have attracted interest as non-destructive metal crack detection (MCD) devices due to their low cost, simple fabrication, potential miniaturization, noncontact nature, and capability for remote detection. However, the development of multi-crack sensors of a suitable size and quality factor (Q-factor) remains a challenge. In the present study, we propose a multi-MCD sensor that combines a higher-mode substrate-integrated waveguide (SIW) and complementary split-ring resonators (CSRRs). In order to increase the Q-factor, the device is miniaturized; the MCD is facilitated; and two independent CSRRs are loaded onto the SIW, where the electromagnetic field is concentrated. The concentrated electromagnetic field of the SIW improves the Q-factor of the CSRRs, and each CSRR creates its own resonance and produces a miniaturizing effect by activating the sensor below the cut-off frequency of the SIW. The proposed multi-MCD sensor is numerically and experimentally demonstrated for cracks with different widths and depths. The fabricated sensor with a TE20-mode SIW and CSRRs is able to efficiently detect two sub-millimeter metal cracks simultaneously with a high Q-factor of 281.