The invention relates to a cross-operation unit scheduling method with a batching machine. The cross-operation unit scheduling method comprises the following steps of: 1, defining three information elements with different structures; 2, initializing the information elements; 3, assigning each process before a batching process of each part to a machine according to a machining order; 4, ordering the processes of each machine according to a time order; 5, batching and scheduling the parts; 6, assigning each process of each part after the batching process to the machine according to the machining order; 7, ordering the processes of each machine according to the time order; 8, updating the information elements according to a obtained solution; and 9, if a circulation frequency reaches an upper limit, or an optimal solution is unchanged for continuous times, finishing; and otherwise, turning to the step 2. With the adoption of the cross-operation unit scheduling method provided by the invention, the part cross-unit scheduling problem in a production process can be solved; and the integrated scheduling of a batching process and a non-batching process in the production process can be treated, and the operation efficiency can be ensured.