A bi-tunable hexagonal boron nitride (hBN)-based metasurface with bi-functional phonon-induced transparency (PIT) and nearly perfect resonant absorption features in the mid-infrared (MIR) range is proposed. The metasurface, that is composed of axially symmetric hBN rings, is separated from a uniform thin vanadium dioxide (VO2) film with a SiO2 spacing layer and is integrated with a top graphene sheet. For the insulating phase of VO2 (i-VO2), PIT with an 80% transmission contrast ratio is observed inside the reststrahlen (RS) band of hBN due to the support of hyperbolic phonon polaritons. A considerably large group delay of 9.5 ps and up to 1.8 THz RIU−1 frequency shift per refractive index unit is also achieved for the i-VO2 case. On the other hand, it is found that for the metallic phase of VO2 (m-VO2), light transmission is prohibited and nearly perfect resonant absorption peaks are appeared inside the RS band of hBN. Finally, by integrating the hBN-based metasurface into the graphene sheet on the top, a tunable PIT-like effect and nearly perfect light absorption is achieved duo to the hybridization of graphene plasmons and hBN phonons. This leads to a modulation depth as high as 87% in the transmission (i-VO2) and 62% in the absorption (m-VO2) responses. Our findings offer a tunable and bi-functional device that is practical for MIR slow-light, sensing, and thermal emission applications.