In this study, the efficiency and beam quality deteriorations in double-cladding fiber (DCF) amplifiers induced by core misalignment of series fusion splices are investigated. The losses of guide modes and power conversions between fundamental mode and high order modes (HOM) are well described according to mode coupling theory. Furthermore, a typical fiber amplifier with three fusion splices and bending mode-selection is established to discuss the mechanism of deteriorations in total systems. Mode competition theory is also introduced to describe different modes powers and beam quality changes with fiber length. Based on these calculations, the accumulations of deterioration caused by series fusion splices are intuitively illustrated. These simulations of laser performance show good accordance with the experimental results. An effective method to significantly enhance the performance of the fiber amplifier is also shown and discussed.