Due to the extremely high pressures in the deep sea, heavy ballast tanks and pressure compensating hydraulic tanks are typically required to support the operation of classic buoyancy controls. Buoyancy control systems driven by phase-change materials (PCM) have unique advantages over conventional hydraulically actuated buoyancy control systems, including high adaptability for deep-sea exploration and simple, lightweight, and compact structures. Inspired by this, a buoyancy control module (BCM) was designed with flexible material as the shell. Instead of a conventional mechanical system, the device uses an electric heating drive to control buoyancy by heating and cooling the PCM. Based on the principle of pressure compensation, this device can adjust the buoyancy of a small underwater vehicle in a deep-sea high-pressure environment. The BCM successfully adjusts the buoyancy to lift itself up and down in the South China Sea at a depth of 3223 m. The performance of the phase-change BCM to control buoyancy under high pressure is validated by systematic experiments and theoretical analysis. Our work proposes a flexible scheme for the design of a deep-sea phase-change-driven BCM and highlights its potential application in deep-sea micro-mechanical systems, especially soft robots.