The complex microspheres based on alginate (AL) and soy protein isolate (SPI) were prepared by solution blending and then Ca 2þ crosslinking, and their function as drug carrier was explored as well. The effects of composition on the structures of microspheres were studied, and the XRD results proved the miscibility between components. Meanwhile, FTIR results suggested that such miscibility was driven by strong hydrogen bonding. Especially, the complex microsphere with equal content of AL and SPI had the best miscibility by morphological analysis, shown as a smooth and uniform surface of SEM images. The controlled release function of the complex microspheres was verified using theophylline as a drug model, that is, the swelling and drug release were affected by pH conditions and showed obvious differences under given pH of stomach, intestine, and colon. Moreover, the intestine and colon may be optimal site for prompt release of drugs. Except for the attribution of AL component to pH sensitivity, the complex microspheres also inherited the bioactivity of SPI component, which may lower irritants of drug to the tissues in body.