Self-assembling peptide-based materials are playing an important role in fabricating drug delivery carriers; however, they are often limited by several challenges, such as precise structure modulation, desirable nanoscale size, and sufficient circulation lifetime in the body. To address this issue, herein one type of injectable dipeptide-based nanocarriers with well modulated size and structure has been developed by adjusting glutaraldehyde (GA)-assisted cationic dipeptide (CDP) assembly. After loading a model photosensitive drug (Ce6) and further decorating CDP nanoparticles (NPs) with heparin polymers (Hep), the desired dipeptide-based NPs are achieved with an average diameter of 100 rim and surface charge of -25 mV, which are favorable for the enhanced permeability and retention effects. Significantly, the dipeptide-based NPs with Ce6 loading have a longer circulation lifetime against opsonization than free Ce6 solution, and subsequently, they achieve the best anticancer efficiency in vivo. They do not cause body weight loss or induce bad immune activation in organs, implying good biosafety of the designed carriers. Taken together, dipeptide-based delivery carriers through GA-assisted assembly may provide a new alternative for developing precisely controlled nanostructures toward effective antitumor therapy.