The invention discloses a method for determining through capacity and service level in channel running. The method comprises the following steps of: defining a calculation formula of the through capacity and service level in channel running; calculating a weighted average tonnage of navigable ships according to ship flow data of control sections; calculating ship fields of ascending and descending ships through combining the weighted average tonnage and utilizing a ship field calculation formula of ascending ships and a ship field calculation formula of descending ships; substituting the weighted average tonnage of the ships and ship field calculated values of the ascending and descending ships into the calculation formula of the through capacity and service level in channel running, thereby determining the through capacity and service level in channel running. The method disclosed by the invention can provide important basis for the design and running of channels, and can be widely applied in water transportation engineering.