We propose a novel humidity measurement system that applies calcium (Ca)-modified silk to the Capacitive Micromachined Ultrasonic Transducer (CMUT) membrane. Due to Ca ions serving as water-capturing points, the Ca-modified silk film absorbs water molecules from the environment. By functionalizing the CMUT membrane with silk, a resonant frequency shift occurs with the change of the relative humidity (RH), and the developed CMUT sensor successfully measured the relative humidity with high sensitivity.