Objective To analyze the clinical efficacy of the standard channel percutaneous nephrolithotomy lithotripsy and percutaneous nephrolithotomy microchannel lithotripsy for the treatment of kidney stones. Methods 60 patients with kidney stones treated in our hospital urology from June 2014 to June 2015 were selected and divided into observation group and control group with 30 cases of each group depending on the surgical methods. Patients in observation group were undentwent microchannels percutaneous nephrolithotomy surgery whilc patients in control group were undent standard channel percutaneous nephrolithotomy surgery. Clinical efficacy and complications were observed and analyzed between groups. Results The patient's operation time, hospital stay, early ambulation time, hospital costs of observation group were significantly lower than those of control group, the difference was statistically significant (P <0.05). The difference of complications and stone clearance rate between two groups was not statistically significant (P>0.05). Conclusion The surgical treatment of kidney stones, the therapeutic effect of microchannel percutaneous nephrolithotomy surgery was significantly better than the standard channel percutaneous nephrolithotomy surgery, which can shorten the hospital stay, reduce hospital costs of patients, bleeding less, and reduce the suffering of patients.