Future surveys will provide a deeper understanding of dark energy, dark matter, and early universe physics through the measurements of large scale structure. In particular, the baryon acoustic oscillation (BAO) method and the redshift-space distortion (RSD) method aim to achieve sub-percent precision on cosmological parameters. Understanding and reducing the systematics caused by the non-linear evolution of gravitational structures and galaxy formation and evolution is crucial for future galaxy spectroscopic surveys. Over the course of this thesis, I develop the tools necessary to understand and quantify these systematic effects, and present a series of applications relevant to future surveys.
I first constructed mock catalogs using the N-body simulations with a reduced number of time steps for future galaxy surveys. Then, I investigated the effects of galaxy bias on the BAO peak and the robustness of the reconstruction method, which is a standard technique used in the BAO measurements to reduce the error. We tested whether the reconstruction method could be applicable to the RSD method to test gravity models. In addition to these studies on large scales, I also explored how assembly history of dark matter halos affects its internal structure and clustering on small scales, including a first measurement of the scale dependence of this effect. These effects of the assembly history on small scales can be a potential source of systematics for future galaxy surveys.