Cross-regulation is one of the critical challenges in single-input and multi-output converters. In this study, new design guidelines and an analytical model for studying the cross-regulation between the dual-outputs of the fly-buck converter are proposed. A small-signal AC model is first established to obtain control over the output and to determine the cross-influence transfer functions of the system. Then, a load regulation coefficient and method for analysing the cross-regulation while considering the load magnitude and load change are proposed to study the characteristics of the fly-buck converter. Finally, to demonstrate the rationality behind the influencing factors over cross-regulation based on the resulting characteristics, a fly-buck converter with double control variables and lower cross-regulation is designed. Simulations and experimental prototypes are implemented to demonstrate the effectiveness of the proposed theoretical analysis.