Povidone-iodine (PI) is a common antiseptic reagent which is used for skin infections and wound healing. The control release of PI is quite important to heal the deep and intense wounds. Herein, the preparation of biodegradable pectin@carboxymethyl pullulan (Pe@CMP) hydrogel was carried out and applied for controllable release of PI. CMP was synthesized by interaction of monochloroacetic acid with pullulan at different ratios. The Pe@CMP hydrogel was then prepared by crosslinking of pectin with CMP in presence of glutaraldehyde as cross linker. After carboxymethylation, COOH contents were enlarged to be 24.2–51.2 mmol/kg and degree of substitution was 0.44–0.93. The rheological properties of Pe@CMP hydrogel were enlarged by increment of pectin ratio. Swelling ratio in water (16.0–18.0%) was higher than that of artificial sweat (11.7–13.2%). Pe@CMP hydrogel containing 20% pectin, exhibited the lowest release and 57.7% from PI was released within 360 min. The biological activity of the released PI was monitored to be highly efficient. The kinetic of release was fitted well to the first ordered reaction and Higuchi models. The mechanism of release was explained by the swelling of hydrogel. The networked structure of hydrogel was opened by swelling and PI was released from the outer pores followed by inner pores, achieving the controllable release.