A highly sensitive photoacoustic detection system using a differential Helmholtz resonator (DHR) combined with a Herriott multipass cell is presented, and its implementation to sub-ppm level carbon dioxide (CO2) detection is demonstrated. Through the utilization of erbium-doped optical fiber amplifier (EDFA), the laser power was amplified to 150 mW. Within the multipass cell, a total of 22 reflections occurred, contributing to an impressive 33.6 times improvement in the system sensitivity. The normalized noise equivalent absorption coefficient (NNEA) was 8.64 × 10-11 cm-1·W·Hz-1/2 [signal-to-noise ratio, (SNR) = 1] and according to the Allan variance analysis, a minimum detection limit of 500 ppb could be achieved for CO2 at 1204 s, which demonstrates the long-term stability of the system. The system was applied to detect the respiration of rice and upland rice seeds. It is demonstrated that the system can monitor and distinguish the respiration intensity and respiration rate of different seeds in real time.