In a gene sequencing system, the ensquared energy is an important parameter for realizing accurate recognition for the base. Nevertheless, the displacement between wafer and camera, which is caused by vibration and position error of wafer stage while photographing, will decrease the image quality and further influence the ensquared energy. This study establishes the relationship model between the dynamic factors and ensquared energy. Static and dynamic experiments are carried out on the sequencing platform. The results reveal that the ensquared energy has linear relationship with the location standard deviation of the wafer stage. If the ensquared energy value is required larger than 65%, the location standard deviation should be controlled below 140 nm. Meanwhile, the ensquared energy calculated by using the DNA nanoball image collected in the dynamic experiment is in accordance with the experimental conclusion. The dynamic performance parameters of the wafer stage in the gene sequencing system can be allocated reasonably.