Abstract： Objective To quantitative analysis the difference of organ contour using planning CT and kilovolt cone beam CT (KVCBCT) deformable registration.Methods One set planning CT image and ten sets of KVCBCT image of one patient were choose and total five patients.Organ contour were automatic outlined to using deformable registration.To compare the organ contours different of deformable registration (DR) and rigid registration (RR).Statistic analysis was executed with paired t-test for dice similarity coefficient (DSC) value and sensitiveness (SENS) value.Results The DSC value of body,left,right lung,heart and spinal respectively:0.971 and 0.980 ( t =3.89,P =0.000 ),0.836 and 0.873 ( t =4.41,P =0.000),0.873 and 0.888 ( t =3.88,P =0.000 ),0.738 and 0.764 ( t =4.83,P =0.000 ),0.666 and 0.677 ( t =2.04,P =0.047 ).The SENS value:0.975 and 0.981 ( t =1.41,P =0.003 ),0.914 and 0.803(t=-6.88,P=0.000),0.926 and 0.800(t=-7.06,P=0.045),0.782 and 0.708(t=-2.50,P=0.040),0.625 and 0.796 (t =-9.09,P =0.000).Conclusions RR is at a competitive disadvantage in terms of organ contour outline.The body,left and right lung that are used DR have advantage over the heart and spinal.