Incision of internal sphincter is often used for the treatment of chronic anal cleft. This study was to compare two approaches- lateral position incision vs. in-situ incision for their effect on anal function. The 160 patients were randomly divided to two groups and received operation accordingly. Patients’ rectal pressures, rectal sensation functions, governing of anal fluid were monitored before and after operation. Results showed that in-situ incision has greater adversary impact on anal function than lateral position incision.