A control equipment and a control method of a stepper are provided. The control equipment of the stepper includes an input device, a generating device and a processing device. The input device is configured to input a plurality of sample development patterns. The sample development patterns are obtained according to a plurality of sample focal length values. The generating device is configured to generate a plurality of generative categories corresponding to a plurality of generative focal length values by using a depth learning algorithm. The processing device is configured to analyze an estimated focal length value of the online development pattern according to the generative categories.