A method for automatically checking a sequence of loading boats and batches for a semiconductor manufacturing process is provided. According to a developed logic, a loading sequence is automatically calculated by a system. By comparing the actual loading sequence with the calculated sequence when the boats are entering, it is ensured that no errors occur when loading the boats in the batches. When loading the boats in the batches, operators can truly load the boats in the batches according to the entering sequence together with the current confirmation mechanism, so as to ensure the boat positions for the loaded materials to be correct. The method for automatically checking the sequence of loading boats and batches is further capable of calculating the loading sequence through the developed logic by automatically determining runnable boat positions for the material after recording a parameter for detecting a previous boat by the system.