The process of single-atom transfer in strongly coupled cavity quantum electrodynamics (QED) with free falling atoms is investigated by experiment and Monte Carlo simulation. We conduct the simulation of the whole physical process and give the corresponding experimental results. In experiment, a high finesse optical cavity is used for real-time detection of the single-atom transits from which the interaction information between single atoms and cavity can be extracted, including the transmission spectra of the cavity strongly coupled to single atoms, the interaction duration of the single atoms in the mode, the probability distribution of atom arrival time and the atomic kinetic energy distribution when arriving at the mode. All these can be completely derived from the transmission spectra of the different initial status. An intracavity far-off resonance trap (FORT) has been established and the single-atom trapping time inside the cavity is about 5 ms which is about 30 times longer than that without FORT. This study gives the detailed analysis of the whole procedure of free-falling atom transfer in cavity QED system and is helpful for optimizing the experimental parameters and design.