Single level tunneling model has been the most popular model system in both the experimental and theoretical study of molecular junctions. We performed a detailed simulation study on the performance of the single level tunneling model in analyzing the charge transport mechanism of molecular junctions. Three different modeling methods, including the numerical integration of the Landauer formula and two approximated analytical formulas that are extensively used for extracting key transport parameters from current–voltage (I-V) characteristics, i.e. the energy offset and the coupling between molecule and electrode, were compared and evaluated for their applicability. The simulation of I-V plots shows that the applicability of the two approximated analytical models is energy offset and coupling strength dependent. Model fitting based on the three methods performed on experimental data attained from representative literature papers revealed that the two approximated analytical methods are neither suitable for the situation of small coupling strength and low energy offset, and they also deviated from the exact results at high bias. We finally provided a phase map of the applicability of different modeling methods as a guide for their proper usage in charge transport study in molecular devices.