Manufacturing and agricultural industries use manual methods to count materials. This leads to low accuracy and inefficiency. This paper proposes a secondary counting method that combines main and differential counting. The area-fill identification algorithm is applied to mark the counted materials. To verify the effectiveness of the proposed counting algorithm, numbers of countings are conducted for different materials, such as the screws, hole gaskets, beans, jujube, etc. The results show that the counting accuracy reaches 98% for materials with size of 2—20 mm. The method has delivered a high-efficiency and high-accuracy automatic intelligent counting, with a wide range of application prospects and reference value.