Phonon modes at microwave frequencies can be cooled to their quantum ground state using conventional cryogenic refrigeration, providing a convenient way to study and manipulate quantum states at the single phonon level. Phonons are of particular interest because mechanical deformations can mediate interactions with a wide range of different quantum systems, including solid-state defects, superconducting qubits, and optical photons when using optomechanically active constructs. Phonons, thus, hold promise for quantum-focused applications as diverse as sensing, information processing, and communication. In this thesis, we describe a piezoelectric quantum bulk acoustic resonator with a 4.88 GHz resonant frequency, which, at cryogenic temperatures, displays large electromechanical coupling strength combined with a high intrinsic mechanical quality factor $Q_i \sim 4.3 \times 10^4$. Using a recently developed flip-chip technique, we couple this resonator to a superconducting qubit on a separate die and demonstrate the quantum control of the mechanics in the coupled system. The resonator lifetime at a single phonon level is measured, which yields a $Q_i \sim 5.43 \times 10^3$. This lower quality factor at a single phonon level is likely due to the two-level system (TLS) defects contamination in the device. To test whether this dissipation comes from the TLS defects, a hole-burning technique is implemented to saturate those defects. As a result, the resonator quality factor is enhanced back to $Q_i \sim 3 \times 10^4$, which demonstrates that TLS defects contribute the dissipation significantly in our device.