The invention discloses a process for cleaning the surface of a piston rod. The process comprises the following steps: 1. racking, 2. degreasing, 3. neutralization, 4. washing, 5. water-based anti-rust treatment, 6. drying, 7. surface conditioning, 8. phosphorization, 9. washing, 10. water-based anti-rust treatment, and 11. room-temperature draining. The process has the following advantages: in the degreasing procedure, the overall rust of the rod is cleaned, and an ultrasonic device is arranged around a groove body, for accelerating rust cleaning; in the neutralization procedure, the overall particle impurities of the rod are cleaned, and the residual solution in the previous procedure is subjected to neutralization treatment; in the washing procedure, the residual solution in the previous procedure is cleaned, and prevented from being brought in the next procedure; in the anti-rust treatment procedure, a layer of anti-rust film on the surface in an activated state, of the rod, is ensured; in the phosphorization procedure, the end surface of a piston is phosphorized, then medicine residues on the surface are cleaned through washing, then the anti-rust treatment is carried out, and the whole cleaning process is completed.