Malachite Cu2(CO3)(OH)2 is a common hydroxycarbonate that contains about 15.3 wt % H2O. Its structural chemistry sheds light on other hydroxyl minerals that play a role in the water recycling of our planet. Here using Raman and infrared spectroscopy measurements, we studied the vibrational characteristics and structural evolution of malachite in a diamond anvil cell at room temperature (25 °C) up to ~29 GPa. Three types of vibrations were analyzed including Cu–O vibrations (300–600 cm−1), [CO3]2− vibrations (700–1600 cm−1), and O–H stretches (3200–3500 cm−1). We present novel observations of mode discontinuities at pressures of ~7, ~15, and ~23 GPa, suggesting three phase transitions, respectively. First, pressure has a great effect on the degree of deformation of the [CuO6] octahedron, as is manifested by the various shifting slopes of the Cu–O modes. [CuO6] deformation results in a rotation of the structural unit and accordingly a phase transition at ~7 GPa. Upon compression to ~15 GPa, the O–H bands redshift progressively with significant broadness, indicative of an enhancement of the hydrogen bonding, a shortening of the O···O distance, and possibly somewhat of a desymmetrization of the O–H···O bond. O–H mode hardening is identified above ~15 GPa coupled with a growth in the amplitude of the lower-energy bands. These observations can be interpreted as some reorientation or reordering of the hydrogen bonding. A further increment of pressure leads to a change in the overall compression mechanism of the structure at ~23 GPa, which is characterized by the blueshift of the O–H stretches and the softening of the O–C–O in-plane bending bands. The hydrogen bonding weakens due to a substantial enhancement of the Cu–H repulsion effect, and the O···O bond length shows no further shortening. In addition, the change in the local geometry of hydrogen is also induced by the softening of the [CO3]2− units. In this regard we may expect malachite and other analogous hydroxyl minerals as capable of transporting water downward towards the Earth’s transition zone (~23 GPa). Our results furnish our knowledge on the chemistry of hydrogen bonding at mantle conditions and open a new window in understanding the synergistic relations of water and carbon recycling in the deep Earth.