The optimization of operation scheme of through freight train from container central station considering fluctuating container throughput is proposed. The objective function intends to minimize the total time of container accumulation and train reformation. The model considers some constraints including the station classification capacity, the classification tracks number, and the container flow formation scheme uniqueness. The daily average container throughput is counted, and the formation plan of through freight train from container central station with certain container throughput is obtained. Then, the daily dynamic container throughput is directly adopted to establish the operation scheme of through freight train from container central station with fluctuating container throughput. Afterwards, a method of transforming random constraints to deterministic constraints is developed to deal with the daily dynamic container throughput, and a meta-heuristic based on filtering-updating-connecting wagon flow sequence is given to obtain the container train operation scheme. Finally, the experimental scenarios are given to test the through train operation scheme models with daily average container throughput and daily dynamic container throughput. Under the container throughput fluctuation range of ±10%, ±15%, ±20%, and ±25%, the feasibility measure of the model with daily average container throughput is respectively 77.2%, 72.4%, 68.4%, and 51.6%. However, the feasibility measure of the model with daily dynamic container throughput arrives at respectively 96 .0%, 92.8%, 88.2%, and 77.2%. Obviously, the latter has more advantages.