Earth to air heat exchangers are widely utilized to cool or heat passive buildings for energy savings. They often need to deal with high humidity air conditions, especially in the greenhouse due to plant transpiration, and the condensation phenomenon is frequently observed during the cooling process. To evaluate the effect of humidity and condensation on thermal performance, a three dimensional computational fluid dynamic (3D-CFD) model was developed. The distribution of relative humidity in each pipe was investigated, and the impact of inlet air relative humidity on the integrated performance of the earth to air heat exchanger was discussed. The effects of inlet air temperature and volume flow rate were also analyzed. Moreover, the influence of the heat exchanger configurations on the performance of the air condensation was researched. The results indicated that condensation had few effects on the airflow distribution uniformity of the earth to air heat exchanger, while it acted observably on the thermal performance. In addition, humid air in a small diameter pipe tended to condense more easily. Humidity and condensation should be taken into consideration for the design of earth to air heat exchangers in greenhouses during engineering applications.