In this study, we introduce a sensing platform based on plasmonic metamaterial absorbers (MAs) with dielectric nanopedestals for the ultrasensitive detection of monolayer biomolecules. MAs with nanopedestals, which allow access to extremely high near-field intensities forming on the top and bottom of nanoantennas that further enhance molecular sensing signals, consist of cross-shaped gold (Au) nanoantennas on dielectric nanopedestals and an Au layer as a mirror layer. The sensing characteristics of the MAs with nanopedestals are compared with control MAs using an unetched dielectric spacer. To provide strong coupling between the molecular vibrations of the target 1-octacanethiol (ODT) molecules and plasmonic resonance from the MAs, the dimensions of the cross-antennas are properly designed and the MAs fabricated by using nanoimprint lithography. Temporal coupled-mode theory is used to analyze the experimentally measured absorption spectra containing the enhanced vibrational signatures of molecules of the ODT monolayer. Based on MAs with nanopedestals, the molecular sensing signal is enhanced over four times compared with that of the control MAs. The proposed structure based on MAs with nanopedestals may provide a promising sensing platform for future applications of ultrasensitive biological and chemical sensing and detection.