The objective of this study is to numerically investigate the effect of cryogenic intake air temperature on the in-cylinder temperature and formation of exhaust emissions in a CI engine. The experimental setup was consisted of a single-cylinder diesel engine. The intake air temperature was varied from 18 °C to 40 °C, which was controlled by cooler and heater. Submodels were applied for the simulations of physical/chemical phenomenon of spray and combustion behaviors. The intake air temperature in numerical condition was varied from −18 °C to 18 °C. The numerical results were validated with experimental results for the reliability of this work. The results of this work were compared in terms of cylinder pressure, rate of heat release (ROHR), indicated specific nitrogen oxide (ISNO), indicated specific carbon monoxide (ISCO), ignition delay, in-cylinder temperature distributions, equivalence ratio distributions, NO mass fraction, and CO mass fraction. When the intake air temperature was decreased in steps of 9 °C, the cylinder temperature and cylinder pressure were decreased in steps of about 14.5 °C and 0.05 MPa, respectively. In all cases, the area where the NO formed in the cylinder was identified with the area of the high equivalence ratio and temperature in the cylinder. The amount of CO generation shows the similar distributions in the cylinder according to the intake air temperature conditions. However, the oxidation rate of formed CO under the low intake air temperature was lower than those of the high intake air temperature.