Motivated by the recent progress of high-frequency ultrasonic measurements, we propose a theory of magnetoacoustic resonance as a microscopic probe for quadrupole degrees of freedom hidden in magnetic materials. A local strain driven by an acoustic wave couples to electronic states of a magnetic ion through various quadrupole-strain couplings, and this provides a periodically time-dependent oscillating field. As a typical two-level system with the quadrupole, we consider a non-Kramers doublet and investigate single- and multiphonon-mediated transition processes on the basis of the Floquet theory. An analytic form of the transition probability is derived within the weak coupling theory, which helps us analyze the magnetoacoustic quadrupole resonance. We apply the theory to realistic non-Kramers doublet systems for the f2 configuration in Oh and D4h symmetries, and discuss how to identify the relevant quadrupole by controlling the quadrupole-strain coupling with an applied magnetic field in ultrasonic measurements.