The high-quality development of the Yellow River Basin is still facing the issue of imbalance and inadequacy, and it urgently requires the backing and assistance of a well-coordinated and efficient comprehensive transportation network system. Based on this purpose, this study uses a composite system synergy degree model incorporating “mode dimension + regional dimension” to analyze the evolution of this network. The results indicate the following: (1) Railway and air transportation surpass highway transportation in growth and synergy, though overall system synergy is still low. (2) Downstream areas are gradually taking the lead, and the orderliness of each subsystem is gradually becoming consistent. The complexity and variability of the composite system’s synergy are high, with an overall low level of synergy. Overall, despite improvements in service capacity and quality, better integration of different transport modes and enhanced cross-regional cooperation are needed. This study reveals and analyzes in depth the complexity of the comprehensive transportation network system in the Yellow River Basin and its spatiotemporal characteristics of synergistic evolution. We propose suggestions for high-quality development at national, regional, and industry levels, fostering the continuous improvement of the system structure, which aids in overcoming the tangible obstacles faced by the high-quality development of the Yellow River Basin.