With the rapid development of supercomputers and the advances of numerical algorithms, nowadays it is possible to study the electronic, structural and dynamical properties of complicated physical systems containing thousands of atoms using density functional theory (DFT). The numerical atomic orbitals are ideal basis sets for large-scale DFT calculations in terms of their small base size and localized characteristic, and can be mostly easily combined with linear scaling methods. Here we introduce a first-principles simulation package “Atomic-orbital Based Ab-initio Computation at UStc (ABACUS)”, developed at the Key Laboratory of Quantum Information, University of Science and Technology of China. This package provides a useful tool to study the electronic, structural and molecular dynamic properties of systems containing up to 1000 atoms. In this paper, we introduce briefly the main algorithms used in the package, including construction of the atomic orbital bases, construction of the Kohn-Sham Hamiltonian in the atomic basis sets, and some details of solving Kohn-Sham equations, including charge mixing, charge extrapolation, smearing etc. We then give some examples calculated using ABACUS: 1) the energy orders of B20 clusters; 2) the structure of bulk Ti with vacancies; 3) the density of states of a model protein; 4) the structure of a piece of DNA containing 12 base pairs, 788 atoms. All results show that the results obtained by ABACUS are in good agreement with either experimental results or results calculated using plane wave basis.