Hydrogel complex scaffolds (hydrogel scaffolds) are prepared by coating precursor solutions onto heparin-modified poly(ϵ-caprolactone) (PCLH) scaffolds followed by subsequent in situ gelation. Here, we show that hydrogel complexation can significantly strengthen the scaffold and slow its degradation. The hydrogel scaffold was implanted into the abdominal aorta of a rat model, and the aneurysm incidence rate of the hydrogel scaffolds sharply decreased compared with that of the hydrogel-free scaffolds. Histological and immunohistological analyses showed that the implanted grafts had good vascular regeneration. The absence of calcification and occurrence of contractile smooth muscle cells (SMCs) at the first month was found in the hydrogel-free PCLH scaffold due to the presence of surface-modified heparin, whereas the hydrogel scaffold exhibited mild calcification and later occurrence of contractile SMCs as the complexed hydrogel covered the fibers and blocked the interaction between heparin and cells. Heparin was further physically encapsulated into the hydrogel before gelation, and its sustainable release was demonstrated by an in vitro release test. A pilot implantation in a rabbit carotid model showed that the encapsulated heparin modulated the scaffold characteristics including anticoagulation, anticalcification, and the early occurrence of contractile SMCs in vivo. Consequently, hydrogel complexation can significantly improve the in vivo regeneration property of the scaffold due to its multiple beneficial characteristics. © 2021 American Chemical Society.