Fiber amplifiers with high power and high pulse energy are strongly in demand for both scientific research and industrial applications. Ytterbium-doped fiber has been an outstanding choice for its broad-gain bandwidth and excellent power conversion efficiencies. In this dissertation, we introduced a compact high power high pulsed energy laser system with chirally coupled core (3C) Yb-doped fibers as the gain media. Traditional standard fibers and photonic crystal fibers are not suitable for compact high power high pulse energy laser systems because of poor higher order modes (HOMs) management and complicated air-hole structure. Newly invented 3C silica fibers solve these problems. A helical side-core around the Yb-doped central core extracts the HOMs from the central core. By adjusting this chirally structure, the core of the 3C fiber can be enlarged and the transverse mode of the fiber can be single mode at certain wavelengths. To simulate the amplification process with high power high pulse energy better, a new modeling method based on a combination of the rate equations and the nonlinear Schrödinger equations is invented. The gain was calculated from rate equations and the pulse evolution was analyzed using nonlinear Schrödinger equation. The simulation provided a good guidance for building compact high power high pulse energy laser systems. To achieve high power and high pulse energy, the system is designed as a two-stage structure. The laser