Inhibition of the maize starch branching enzyme IIb (ZmSBEIIb) significantly alters the amylose content and grain yield in maize. Only a few ZmSBEIIb-interacting proteins involved in the starch branching process have been identified, and the understanding of this mechanism is limited. We report here the successful isolation of an Anoctamin protein, ZmSIP, that binds directly to ZmSBEIIb. In our study, the detection of interaction between ZmSIP and different truncated ZmSBEIIb baits in yeast showed that the full-length ZmSBEIIb is essential for binding. The direct protein–protein interaction could also be found in co-transformed tobacco protoplasts. Moreover, knocking out the ZmSIP gene using the CRISPR/Cas9 system could effectively increase the apparent amylose content but maintain the maize kernel weight. Thus, our results suggest that ZmSIP may be involved in the ZmSBEIIb-mediated amylose synthesis pathway through its physical interaction with ZmSBEIIb.