High energy astrophysics is one of the most active branches in the contemporary astrophysics. It studies astrophysical objects that emit X-ray and γ-ray photons, such as accreting super-massive and stellar-size black holes, and various species of neutron stars. With the operations of many space-borne and ground-based observational facilities, high energy astrophysics has enjoyed rapid development in the past decades. It is foreseen that the field will continue to advance rapidly in the coming decade, with possible ground-breaking discoveries of astrophysical sources in the high-energy neutrino and gravitational wave channels. This Special Issue of Frontiers of Physics is dedicated to a systematic survey of the field of high energy astrophysics as it stands in 2013. 95.85.Nv, 95.85.Pw, 95.85.Ry, 95.85.Sz, 97.60.Lf, 97.60.Jd, 97.80.Jp, 98.62.Js High energy astrophysics is the branch of astrophysics that studies astrophysical objects that emit high energy photons (X-rays and γ-rays), and more generally, emit non-thermal photons outside the traditional optical wavelengths. By studying non-thermal emission in the universe, one can unveil the part of universe that is not in a steady state, usually originating in violent environments near compact objects, such as neutron stars and black holes of different scales. These objects, besides emitting the broad-band non-thermal electromagnetic radiation, are also believed to be emitters of other signals outside the electromagnetic channel. These multi-messenger signals include cosmic rays, neutrinos, and gravitational waves. The field of high energy astrophysics, along with cosmology and planetary sciences, is one of the three most active branches in the contemporary astrophysics. PACS numbersDuring the past decades, the field of high energy astrophysics has enjoyed a rapid development, thanks to an impressive list of space-borne and ground-based observational facilities. The currently operating space missions dedicated to high energy astrophysics include the Chandra X-ray Observatory, the X-ray Multi-Mirror Mission (XMM)-Newton, Suzaku, and the Nuclear