Thinning is a crucial practice in the forest ecosystem management. The soil infiltration rate and water storage capacity of pine-oak mixed forest under three different thinning intensity treatments (15%, 30%, and 60%) were studied in Qinling Mountains of China. The thinning operations had a significant influence on soil infiltration rate and water storage capacity. The soil infiltration rate and water storage capacity in different thinning treatments followed the order of control (nonthinning): <60%, <15%, and <30%. It demonstrated that thinning operation with 30% intensity can substantially improve soil infiltration rate and water storage capacity of pine-oak mixed forest in Qinling Mountains. The soil initial infiltration rate, stable infiltration rate, and average infiltration rate in thinning 30% treatment were significantly increased by 21.1%, 104.6%, and 60.9%, compared with the control. The soil maximal water storage capacity and noncapillary water storage capacity in thinning 30% treatment were significantly improved by 20.1% and 34.3% in contrast to the control. The soil infiltration rate and water storage capacity were significantly higher in the surface layer (0~20 cm) than in the deep layers (20~40 cm and 40~60 cm). We found that the soil property was closely related to soil infiltration rate and water storage capacity.