To improve the normalized transmission of photonic crystal biosensors based on the air-pore structure, the particle swarm optimization algorithm has been adopted to optimize the structure parameters globally in the multi-dimensional space. The optimization process has been performed according to the position-velocity updating equation, in which the coupling structure combining the ring cavity with the line waveguide is regarded as the optimized object, and the scattering air pores, the coupling air pores and the inner air pores are regarded as the optimized variables. Then the sensing property has been analyzed using the optimized structure, in which the coupling area and the inner area have been adopted as the sensing region respectively. The simulation results show that the normalized transmission can be increased from 54% to 92% after optimization and the relationship between shift of the resonant wavelength and the change of the refractive index for the biological sample is linear. And the sensitivity of the inner air pores as the sensing region is higher than those of the general chip and the coupling air pores with the sensitivity more than 950 nm/RIU. The structure optimization method can provide effective guidance for other functional devices and integrated optical waveguide devices.