On the basis of the original well, the slim hole deepening operation can speed up the development progress and reduce the cost. In slim hole deepening operation, it is necessary to mill through the artificial bottom with flat-faced milling shoes. Because of the low milling line speed in the center of the bottom hole, the penetration rate of the milling operation is limited. In order to improve the milling penetration rate at the bottom hole center, a dynamic model of milling shoe-drillstring is established, and the effects of milling shoe diameter, drill collar diameter and rotation speed on the distribution of bottom hole milling line speed are studied. The numerical simulation results show that the diameter of the milling shoe has the greatest influence on the trajectory of the center of the milling shoe, and then affects the distribution of the milling linear velocity. Reducing the size of the milling shoe properly will greatly improve the linear velocity at the bottom of the well and the final penetration rate, and there is an optimal diameter of the milling shoe; the influence of the drill collar is small, but it is unnecessary to use the large-size drill collar. The surface rotating speed will affect the evenness of milling. The greater the rotating speed is, the more uniform the milling will be. If the speed is too small, it is easy to cause less milling around the wellbore. Therefore, it is necessary to increase the time of repairing the well in the later stage as far as possible. Finally, according to the results of numerical simulation, the milling BHA is redesigned, and the field tests of three wells are carried out. The test results show that the improved design can greatly improve the milling rate. The optimal size of milling shoe determined by the experiment is close to the results of numerical simulation, and the penetration rate of milling is three times of the original design. When the size of milling shoe is small, the penetration rate of milling is far higher than the original design. However, it takes a long time to repair the well in the later stage.