The biocompatibility and antibacterial properties of hydroxyapatite (HAp) bioceramics are crucial in medical applications. However, it is still a challenge to control HAp with antibacterial ability while maintaining other biological properties in the development of bioactive bone implants. Herein, we report functional silver ion substituted HAp bioceramics with excellent osteoconductivity and efficient antibacterial activity and propose a stern-interface induced antibacterial mechanism of such bioactive ceramics. In this antibacterial process, the concentration of Ag+ at the stern-interface of Ag/HAp bioceramics is nearly 5 times higher than that in the bulk solution due to the trace dopant Ag+ enrichment in the stern layer of the electric double layer at the negatively charged surface of Ag/HAp bioceramics. Trace Ag-doping in HAp induces a positive shift of zeta potential and increase of hydrophilicity, which may help inhibit bacterial proliferation. The positive osteoblast adhesion, proliferation and differentiation of ultra-trace doped Ag/HAp are also demonstrated through actin cytoskeleton staining, MTT and alkaline phosphatase (ALP) activity assays. This work may enlighten us on the artificial design of novel smart anti-infective bone grafts using ultra-trace functional elements and also suggest its potential applications in orthopedic surgery and bone osseointegration.