The invention belongs to the technical field of mechanical rolling functional unit manufacturing, and provides a ball screw pair cleaning and running-in machine. The ball screw pair cleaning and running-in machine comprises a machine body, a cleaning fluid circulation system and an electric control system; the machine body is used for bearing the entire ball screw pair cleaning and running-in machine; a to-be-cleaned ball screw pair rotates under the driving of a motor; the rotating to-be-cleaned ball screw pair employs nuts of the to-be-cleaned ball screw pair to drive a splash guard body to make reciprocating motion on a linear guide rail pair; a cleaning nozzle is formed in the splash guard body, and circulation cleaning is realized under the control of the electric control system; and the cleaning fluid is used for cyclic utilization of a cleaning fluid. The ball screw pair cleaning and running-in machine is used for automatically realizing the effects of cleaning and running-in on surface residual oil on the ball screw pair, so that the cleaning operating efficiency of the ball screw pair is improved substantially, the labor intensity of cleaning operation of the ball screw pair is relieved, the cleaning quality of the ball screw pair is improved, and the usage amount of the cleaning fluid is reduced. In addition, through reciprocating cleaning and running-in, a cleaning function is exerted on residual oil on the nuts and balls.