Super FR is the fast reactor version of SuperCritical Light Water Reactor (SCWR), which operates under supercritical condition of light water, so that designing the core with high coolant outlet temperature above the pseudo-critical point is possible. To raise the core outlet temperature of Super FR, axially heterogeneous core concept was proposed by the preceding study. It consisted of alternatively arranged two seed layers and two blanket layers (i.e., four-layers core). Furthermore, the core was axially divided to two sections and fuel shuffling was considered in each of the two axial sections independently to improve breeding performance. However, the study assumed the same fuel depletion history along the axial direction of the core, despite the large coolant density change. The core outlet temperature was only 387 C and the Compound System Doubling Time (CSDT) was about 98 years, which was not as short as desired. Hence, this study aims to reveal more comprehensive understanding of the concept of improving the performance of Super FR with fuel shuffling in multi-axial layers through design analyses. A five-layers core is considered, which consists of the lower blanket, lower seed, inner blanket, upper seed, and the upper blanket layers. Influences of the lower blanket/upper blanket discharge burnup on the core characteristics, such as the CSDT, void reactivity, and core outlet temperature have been studied with different coolant inlet temperatures for the first time. Different fuel depletion histories are considered for each of the axial layers with consideration of the axial coolant density change (which had not been considered in the preceding study). The present results show that it is preferable to keep the lower blanket discharge burnup relatively low, compared with that of the upper blanket to improve breeding performance with respect to achieving short CSDT. However, it leads to slight reduction in the core outlet temperature. Based on the sensitivity analyses, a representative design is proposed, which achieves CSDT of 74 years and average core outlet temperature of 492 C, which show significant improvement from the preceding design.