A vertically coupled suspended silicon nitride resonator sensor is experimentally demonstrated, which consists of a bottom-layer un-suspended access waveguide and a top-layer suspended microdisk cavity. The presented sensor can realize a high device sensitivity with a good mechanical stability. For a 40-μm-radius disk, more than 104 quality factor at a wavelength of 1548.98 nm can be obtained with a moderate free-spectral range of 5.66 nm. The device sensitivity is measured with covering different organic liquids, and the sensitivity is about 554 nm/RIU. The fabrication of the proposed three-dimensional sensor is compatible with conventional photolithography process, which would benefit its optical sensing applications.