The human-land-water systems within a river basin are interconnected and exhibit mutually reinforcing relationships. Investigating their coupling coordination degree and influencing factors is crucial for achieving regional high-quality development and ecological civilization construction. Taking the nine provinces in the Yellow River Basin as the study area, the entropy method and a comprehensive evaluation method were employed to measure the index levels of the human system, land system, and water system within the Yellow River Basin from 2013 to 2022. Building upon this foundation, the coupling coordination degree model and fixed effects (FE) model were utilized to analyze and evaluate the spatio-temporal differentiation characteristics of the human-land-water systems coupling coordination degree and its influencing factors at both dual (human-land, human-water, land-water) and ternary (human-land-water) levels. The results indicated that from 2013 to 2022, the overall human-land-water systems in the nine provinces showed steady progress, although the development speeds of the subsystems varied, mostly exhibiting a fluctuating upward trend. Significant spatial disparities existed in the coupling coordination degree across the nine provinces during 2013—2022. By 2022, five provinces (Inner Mongolia, Ningxia, Shanxi, Henan, Shandong) reached an intermediate coordination level, while the other four provinces still had considerable room for development. The coupling coordination degrees of the dual systems (human-land, human-water, land-water) in all provinces also generally showed a year-by-year strengthening trend. Technological investment and rural governance investment positively influenced the coupling coordination degree. Industrial structure upgrading, the degree of openness, fixed asset investment, and government regulatory capacity exerted varying degrees of influence on the coupling coordination degree. In conclusion, against the backdrop of advancing the major national strategy for ecological protection and high-quality development in the Yellow River Basin, differentiated pathways for synergistic human-land-water development should be formulated for the upper, middle, and lower reaches. This would facilitate the rational coordination of multi-system development relationships within the basin and promote healthy and sustainable regional development in the future.