We report the use of 2,6-dimethylphenyl isocyanide (2,6-DMPI) as a spectroscopic probe to study the heterogeneous nucleation and deposition of Pd on Ag nanocubes under different conditions by surface-enhanced Raman scattering. As a major advantage, the spectroscopic analysis can be performed in situ and in real time with the nanoparticles still suspended in the reaction solution. The success of this method relies on the distinctive stretching frequencies (νNC) of the isocyanide group in 2,6-DMPI when it binds to Ag and Pd atoms through σ donation and π-back-donation, respectively. Significantly, we discovered that νNC was sensitive to the arrangement of Pd adatoms on the Ag surface. For example, when the isocyanide group bound to one, two, and three Pd atoms, we would observe the atop, bridge, and hollow configurations, respectively, at different νNC frequencies. As such, the νNC band could serve as a characteristic reporter for the Pd adatoms being deposited onto different types of facets on Ag nanocubes with atomic-level sensitivity. When 2,6-DMPI molecules were introduced into the reaction solution, we further demonstrated in situ tracking of heterogeneous nucleation and early stage deposition of Pd on Ag nanocubes by monitoring the evolution of νNC bands for both Ag and Pd surface atoms as a function of reaction time. This in situ technique opens up the opportunity to investigate the roles played by reaction temperature and the type of Pd(II) precursor in influencing the heterogeneous nucleation and growth of bimetallic nanocrystals. The sensitivity of isocyanide group to Pd atoms helps elucidate some of the details on the reduction, deposition, and diffusion processes involved in heterogeneous nucleation.