Investigations on modeling methods of a CFD wind resource prediction program, WindSim for a ccurate predictions of wind speeds were performed with the field measurements. Meteorological Masts having heights of 40m and 50m were installed at two different sites in complex terrain. The wind speeds and direction were monitored from sensors installed on the masts and recorded for one year. Modeling parameters of WindSim input variables for accurate predictions of wind speeds were investigated by performing cross predictions of wind speeds at the masts using the measured data. Four parameters that most affect the wind speed prediction in WindSim including the size of a topographical map, cell sizes in x and y direction, height distribution factors, and the roughness lengths were studied to find out more suitable input parameters for better wind speed predictions. The parameters were then applied to WindSim to predict the wind speed of another location in complex terrain in Korea for validation. The predicted annual wind speeds were compared with the averaged measured data for one year from meteorological masts installed for this study, and the errors were within 6.9%. The results of the proposed practical study are believed to be very useful to give guidelines to wind engineers for more accurate prediction results and time-saving in predicting wind speed of complex terrain that will be used to predict annual energy production of a virtual wind farm in complex terrain.