The main purpose of this research is to investigate the effect of drilling processes and tool geometry parameters on the hole quality for gun deep drilling. In this study, Taguchi’s orthogonal arrays are firstly used to plan the experiments layout. All experiments are carried on a gun drill machine according to the results of experiments layout. A 12.7-mm-diameter drilled hole is 220 mm in depth. There are twenty areas at every 10-mm distance along each hole axis is planned to measure the surface roughness. The hole quality is estimated by means of the average and the standard deviation of the values of surface roughness. An abductive neutral network is used to modeling the averages as well as the standard deviation of surface roughness between drilling processes and tool geometry parameters, the result showing that it is capable of accuracy in predicting the values of average and the standard deviation of surface roughness. The optimal parameters can be searched for by a conjugate gradient method. Experimental results have shown that optimal parameters can improve about 20% of hole quality.