In this study, the effect of the structure of an ultrafine cryoprobe on its cooling performance was evaluated experimentally and numerically. To clarify the thermodynamic characteristics of the refrigerant in the ultrafine cryoprobe, three ultrafine cryoprobes with different dimensions were manufactured. Additionally, a phase change flow model was developed to estimate the refrigerant condition in a microchannel and evaluate the cooling characteristics of an ultrafine cryoprobe. For validating the numerical model, the results were compared with experimental data and a suitable empirical correlation for a two-phase pressure drop was determined. By calculating the refrigerant condition in an ultrafine cryoprobe, it is clarified that large pressure drops occur in the inner tubes and the refrigerant becomes subcooled owing to heat exchange between the flows in the inner and outer tubes. The temperature differences for three different cryoprobes are reproduced by the developed model. By changing the dimensions of the tubes comprising the ultrafine cryoprobes in the calculation, the lowest temperature can be determined. Additionally, freezing experiments are conducted, and the importance of temperature and vapor quality in ultrafine cryoprobes is represented in the time variation of the frozen region.