A low-temperature drying with fluidized bed dryer (FBD) for wheat germ (WG) stabilization could prevent the loss of nutrients during processing. However, both evaporation and condensation behaviors occurred in sequence during FBD drying of WG. The objective of this study was to develop a theoretical thin-layer model coupling with the macro-heat transfer model and the bubble model for simulating both the dehydration and condensation behaviors of WG during low-temperature drying in the FBD. The experimental data were also collected for the model modification. Changes in the moisture content of WG, the air temperature of FBD chamber, and the temperature of WG during drying with different heating approaches were significantly different. The thermal input of WG drying with short heating time approach was one-third of that of WG drying with a traditional heating approach. The mathematical model developed in this study could predict the changes of the moisture content of WG and provide a good understanding of the condensation phenomena of WG during FBD drying.