Atomic-force microscopy coupled with infrared spectroscopy (AFM-IR) deciphers surface morphology of thin-film polymer blends and composites by simultaneously mapping physical topography and chemical composition. However, acquiring quantitative phase and composition information from multi-component blends can be challenging using AFM-IR due to the possible overlapping infrared absorption bands between different species. Isotope labeling one of the blend components introduces a new type of bond (carbon-deuterium vibration) that can be targeted using AFM-IR and responds at wavelengths sufficiently shifted toward unoccupied regions (around 2200 cm-1). In this project, AFM-IR was used to probe the surface morphology and chemical composition of three polymer blends containing deuterated polystyrene; each blend is expected to exhibit various degrees of miscibility. AFM-IR results successfully demonstrated that deuterium labeling prevents infrared spectral overlap and enables the visualization of blend phases that could not normally be distinguished by other scanning probe techniques. The nanoscale domain composition was resolved by fast infrared spectrum analysis. Overall, we presented isotope labeling as a robust approach for circumventing obstacles preventing the quantitative analysis of multiphase systems by AFM-IR.