Ion desorption efficiency and internal energy transfer were probed and correlated in carbon-based surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) using benzylpyridinium (BP) salt as the thermometer chemical. In a SALDI-MS experiment with a N(2) laser (at 337 nm) used as the excitation light source and with multiwalled carbon nanotubes (CNT), buckminsterfullerene (C(60)), nanoporous graphitic carbon (PGC), non-porous graphite particles (G), highly oriented pyrolytic graphite (HOPG), or nanodiamonds (ND) as the SALDI substrate, both the desorption efficiency in terms of ion intensity of BP and the extent of internal energy transfer to the ions are dependent on the type and size of the carbon substrates. The desorption efficiency (CNT approximately C(60) > PGC > G > HOPG > ND) in general exhibits an opposite trend to the extent of internal energy transfer (CNT < C(60) approximately PGC < G approximately HOPG < ND), suggesting that increasing the extent of internal energy transfer in the SALDI process may not enhance the ion desorption efficiency. This phenomenon cannot be explained by a thermal desorption mechanism, and a non-thermal desorption mechanism is proposed to be involved in the SALDI process. The morphological change of the substrates after the laser irradiation and the high initial velocities of BP ions (1100-1400 ms(-1)) desorbed from the various carbon substrates suggest that phase transition/destruction of substrates is involved in the desorption process. Weaker bonding/interaction and/or a lower melting point of the carbon substrates favor the phase transition/destruction of the SALDI substrates upon laser irradiation, consequently affecting the ion desorption efficiency.