Competition between the CC functional group with the OH group in allyl alcohol and with the CO group in allyl aldehyde in the adsorption and thermal chemistry on Si(100)2×1 has been studied by X-ray photoelectron spectroscopy (XPS) and temperature-programmed desorption (TPD), as well as density-functional theory (DFT) calculations. The similarities found in the C 1s and O 1s spectra for both molecules indicate that the O–H dissociation product for allyl alcohol and [2+2] CO cycloaddition product for allyl aldehyde are preferred over the corresponding [2+2] CC cycloaddition products. Temperature-dependent XPS and TPD studies further show that thermal evolution of these molecules gives rise to the formation of ethylene, acetylene, and propene on Si(100)2×1, with additional CO evolution only from allyl alcohol. The formation of these desorption products also supports that the [2+2] CC cycloaddition reaction does not occur. In addition, the formation of SiC at 1090K is observed for both allyl alcohol and allyl aldehyde. We propose plausible surface-mediated reaction pathways for the formation of these thermal evolution products. The present work illustrates the crucial role of the Si(100)2×1 surface in selective reactions of the Si dimers with the O−H group in allyl alcohol and with the CO group in allyl aldehyde over the CC functional group common to both molecules.