Abstract We propose a novel design of refractive index (RI) sensor array based on ultrahigh sensitivity one dimensional (1D) photonic crystal microfiber (PCMF) cavities, which is referred as photonic crystal microfiber cavity sensors array (PCMF-CSA). The proposed PCMF-CSA consists of multiple channels connected in parallel. A transmission only containing the fundamental mode (FM) resonance of the PCMF cavity sensor for sensing purpose is created by connecting an additional PCMF bandgap filter to a PCMF cavity sensor in series on each channel. Due to the photonic bandgap (PBG) of the PCMF bandgap filter, the other high-order resonances are filtered out. With proper engineering of the PBG, multiple ultrahigh sensitivity PCMF cavity sensors can be integrated into microarrays without resonance overlap, and be detected simultaneously between a single input optical fiber and a single output optical fiber without the need for complicated coupling systems. The concept was demonstrated with 7-channel PCMF cavity sensor array containing PCMF bandgap filters. By using three-dimensional finite-difference time-domain (3D-FDTD) method, the performance of the device was investigated theoretically. The simulation results showed that the sensors on each channels can be monitored simultaneously from a single output spectrum. The numerical calculated RI sensitivities (S) for each sensing channel of the proposal 7-channel PCMF-CSA as high as 647.33 nm/RIU, 666.67 nm/RIU, 662.00 nm/RIU, 676.00 nm/RIU, 674.67 nm/RIU, 659.33 nm/RIU, 679.99 nm/RIU can be achieved, respectively. The average RI sensitivity as high as 666.57 nm/RIU can be obtained. Moreover, the extinction ratios of all resonant peaks exceed 20.0 dB. The crosstalk of all channels is lower than −24.5 dB. To the best of our knowledge, this is the first silica PCMF sensors array geometry based on conventional single mode fiber (SMF) that features both high Q and S, and thus is potentially a promising platform for ultra-sensitive RI-based gas sensing with high parallel-multiplexing capability.