This paper uses the improved bond-based peridynamics (BB PD) method to predict the crack evolution and macroscopic mechanical properties of the hardened cement paste at the micro-scale. Specifically, the prototype micro-elastic brittle (PMB) model is improved by considering an attenuation kernel function and the surface effect correction. Subsequently, the uniaxial tension simulations of hardened cement microstructures generated by μic software are systemically conducted to investigate the influences of the heterogeneity of microstructure, size effect, and water-cement ratio (w/c) on crack growth and mechanical properties, i.e., tensile strength and Young's modulus. The results show that the heterogeneity of the microstructure inevitably will cause the discreteness of the macroscopic properties of the numerical cement paste. Therefore, a statistical method is considered to analyze the mechanical properties of the hardened cement. Moreover, the tensile strength has a remarkable size effect, with the size increase of microstructure, the tensile strength decreases; the simulation results fit well with the existing analytical size effect model, i.e., Weibull size effect model, multifractal scaling law, and Bažant's size effect law. Besides, the higher ratio of w/c is likely to result in lower tensile strength, Young's modulus and premature damage to the cement paste. The predicted macroscopic mechanical properties are in good agreement with the previous simulation and experimental data, which demonstrates the reliability of the improved bond-based peridynamic method in studying the crack initiation and propagation of hardened cement paste.