In order to reduce the influence on the appearance and quality of production on the pecan kernel pouch packaging machine, caused by bag film deviation, we proposed an intelligent control scheme based on fuzzy control. Firstly, the reasons of bag film deviation and the rectification feasibility in the working process of the film-drawing mechanism was analyzed. Furthermore, a model of deviation correction control was designed to detect the offset of the bag film by using the CCD sensor, and the fuzzy control rules were established to adjust the film-drawing velocity and the deviation angle of correcting rod in real time. This could ensure the bag film offset always within the required range. The improved DF-50B2 powder automatic packing machine was used as the test platform to rectify the deviation. In addition, the output effect of fuzzy control system was tested by LabVIEW software. The experimental results showed that the control system had a preferable rectifying effect. When the drawing speed was set at 80 mm/s, the maximum rectification precision of fuzzy control was 0.52 mm, and the packaging weight had no obvious influence on the rectify deviation effect, the film offset increasing with the film-drawing velocity. The control system could accelerate the packaging speed on the premise of ensuring the product’s quality requirements, which also improved the efficiency of packaging machine.