High-lift siphon drainage can release a large number of bubbles. The pipe diameter d≤5 mm should be adopted to form slug flow, so as to prevent the accumulation of air in the siphon process from damaging the long-term performance of siphon drainage. Due to the small pipe diameter and gas-liquid two-phase flow, the existing siphon velocity calculation may have large errors, which affect the rationality of siphon drainage system design. In view of the problem of large error in velocity calculation of small-diameter siphon, the velocity calculation parameters were determined by analyzing the characteristics of siphon flow process. The Barr formula was introduced into the calculation of friction head loss, and full-scale physical model test was carried out. The formula of head loss coefficient suitable for the iterative calculation of siphon velocity was determined, and the calculation method of laminar flow velocity in circular pipe was proposed by using the average head loss of cross-section to reflect the influence of boundary layer. The reduction coefficient was introduced into the Barr formula to reduce the calculation error of velocity in the critical Reynolds number region. Test results of the physical model show that the modified calculation method improved the calculation accuracy of siphon velocity, which can provide reference for engineering application.