Crop economic losses greater than 30% can result from damage caused by pests, diseases, and weeds. Therefore, effective pest and disease control is essential for ensuring high crop yields and economic benefits. Crop pest and disease incidence comprehensively reflect the interaction between harmful organisms, crops, and environmental conditions. The strip intercropping system for soybeans and maize comprises a closely spaced maize strip alternating with a soybean strip consisting of two to six rows. Changes in field configuration can lead to significant changes in microclimate, which, in turn, may alter the pattern of pest and disease incidence. We systematically and comprehensively studied the patterns of pest incidence in this intercropping system and found that major pests, such as maize borers, bean pod borers, and soybean aphids, were suppressed, whereas root rot, bacterial and fungal leaf spots, and viral disease incidence were reduced. Furthermore, beneficial predators and insect pest-parasitoids were enhanced. Lastly, a row ratio of 3:2 or 4:2 was found to be optimal for pest and disease control.