To date, there has been significant interest in determining the extent to which different anticancer drugs delivered through identical nanodrug delivery systems have different drug permeabilities in tumor microenvironment (TME) and thus variable anticancer effects. In this study, we measured variations in drug permeability and the quantity of anticancer drugs delivered through the same nanodrug delivery system in the TME from intratumoral blood vessels. Measurements were conducted with respect to therapy type, including chemotherapy and photodynamic therapy. The results revealed significant variations in drug permeability depth and anticancer drug amounts depending on the drug target and therapeutic approach. Hypoxic cancer cells are the main targets of anticancer drugs as a cause of cancer recurrence; however, anticancer drugs do not reach these cells because of their limited drug permeability. To the best of our knowledge, this is the first study to present a bioenzyme-conjugated nanodrug delivery system with excellent drug permeability that can effectively kill hypoxic cancer cells in the TME.