Healthcare and biosensing have attracted wide attention worldwide, with the development of chip integration technology in recent decades. In terms of compact sensor design with high performance and high accuracy, photonic crystal structures based on Fano resonance offer superior solutions. Here, we design a photonic crystal structure for sensing applications by proposing modeling for a three-cavity-coupling system and derive the transmission expression based on temporal coupled-mode theory (TCMT). The correlations between the structural parameters and the transmission are discussed. Ultimately, the geometry, composed of an air mode cavity, a dielectric mode cavity and a cavity of wide linewidth, is proved to be feasible for simultaneous sensing of refractive index (RI) and temperature (T). For the air mode cavity, the RI and T sensitivities are 523 nm/RIU and 2.5 pm/K, respectively. For the dielectric mode cavity, the RI and T sensitivities are 145 nm/RIU and 60.0 pm/K, respectively. The total footprint of the geometry is only 14 × 2.6 (length × width) µm2. Moreover, the deviation ratios of the proposed sensor are approximately 0.6% and 0.4% for RI and T, respectively. Compared with the researches lately published, the sensor exhibits compact footprint and high accuracy. Therefore, we believe the proposed sensor will contribute to the future compact lab-on-chip detection system design.