According to the imbalance problem of the observed upstream and downstream annual runoff data, this paper put forward the conditional adjustment calculation method using the least square condition adjustment model, and discussed the principle of the least square method, the mathematical model and the deduction calculation process of the annual runoff data by conditional adjustment method. By the calculation results of the 8-year observed annual runoff data and the water change amount at the 6 hydrometry stations in the reach between the Huayuankou and Lijin hydrometry stations, it shows that the conditional adjustment can eliminate the contradiction between the annual runoff data of the various hydrometry stations and the water change amount of the adjacent hydromety stations, so as to achieve the special and yearly water amount balance, give the scientific accuracy assessment, and make the adjusted runoff data more reliable and practical.