BEAMing (beads, emulsion, amplification, and magnetics) is a high sensitive emulsion digital PCR (polymerase chain reaction) technology. Target beads obtained via BEAMing can be used to determine the copy number of target DNA population. However, the existing beads counting process requires specialized instrument, which has increased the detection costs. Here we developed an easy and low cost beads counting method combined with microspheres and micropillar array chips. Through counting the chip-trapped polystyrene microspheres which have captured the target magnetic beads, we could easily infer the number of target magnetic beads and the copy number of target DNA. The trapping mechanism was based on the difference of microsphere diameter and pillar intervals. Fabrication of the chip was simple and low-cost. This method has reduced the difficulty of beads counting process in BEAMing and may promote the applications of BEAMing in clinical filed.