This study investigated organic compounds in a cleanroom air and on silicon (Si) wafer surfaces using gas chromatograph-mass spectroscopy (GC-MS) and thermal desorption-atmospheric pressure ionization mass spectroscopy (TD-APIMS). Si wafers with hydrogen terminate and with native oxygen exposed in the cleanroom air were analyzed. As an analytical result using TD-APIMS, chained hydrocarbons such as C2-C5 alkanes were detected with higher values than phthalates such as DOP and DBP from Si wafers with hydrogen terminate and with native oxygen exposed in the cleanroom air. The adsorption mechanisms of organic compounds on Si wafers were discussed by thermal desorption spectra. Based on these results, the adsorption hierarchy model of organic compounds on Si wafer surfaces was proposed.