Surface plasmons have proven their ability to boost the sensitivity of mid-infrared hyperspectral imaging by enhancing light-matter interactions. Surface phonons, a counterpart technology to plasmons, present unclear contributions to hyperspectral imaging. Here, we investigate this by developing a plasmon-phonon hyperspectral imaging system that uses asymmetric cross-shaped nanoantennas composed of stacked plasmon-phonon materials. The phonon modes within this system, controlled by light polarization, capture molecular refractive index intensity and lineshape features, distinct from those observed with plasmons, enabling more precise and sensitive molecule identification. In a deep learning-assisted imaging demonstration of severe acute respiratory syndrome coronavirus (SARS-CoV), phonons exhibit enhanced identification capabilities (230,400 spectra/s), facilitating the de-overlapping and observation of the spatial distribution of two mixed SARS-CoV spike proteins. In addition, the plasmon-phonon system demonstrates increased identification accuracy (93%), heightened sensitivity, and enhanced detection limits (down to molecule monolayers). These findings extend phonon polaritonics to hyperspectral imaging, promising applications in imaging-guided molecule screening and pharmaceutical analysis.