Horizon Run 5 (HR5) is a cosmological hydrodynamical simulation that captures the properties of the universe on a Gpc scale while achieving a resolution of 1 kpc. Inside the simulation box, we zoom in on a high-resolution cuboid region with a volume of 1049 × 119 × 127 cMpc3. The subgrid physics chosen to model galaxy formation includes radiative heating/cooling, UV background, star formation, supernova feedback, chemical evolution tracking the enrichment of oxygen and iron, the growth of supermassive black holes, and feedback from active galactic nuclei in the form of a dual jet-heating mode. For this simulation, we implemented a hybrid MPI-OpenMP version of RAMSES, specifically targeted for modern many-core many-thread parallel architectures. In addition to the traditional simulation snapshots, lightcone data were generated on the fly. For the post-processing, we extended the friends-of-friend algorithm and developed a new galaxy finder PGalF to analyze the outputs of HR5. The simulation successfully reproduces observations, such as the cosmic star formation history and connectivity of galaxy distribution, We identify cosmological structures at a wide range of scales, from filaments with a length of several cMpc, to voids with a radius of ∼ 100 cMpc. The simulation also indicates that hydrodynamical effects on small scales impact galaxy clustering up to very large scales near and beyond the baryonic acoustic oscillation scale. Hence, caution should be taken when using that scale as a cosmic standard ruler: one needs to carefully understand the corresponding biases. The simulation is expected to be an invaluable asset for the interpretation of upcoming deep surveys of the universe.