<p>The economic system of the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) constitutes a complex nonlinear system. The relationships among the system and its constituent variables are highly intricate. Linear methods prove inadequate for understanding the inherent laws of the regional economy within the GBA. Consequently, a nonlinear rescaled range fractal analysis was employed to perform an empirical analysis of the macroeconomic dynamics of the GBA from 2000 to 2023. The analysis reveals two structural imbalance issues. A persistent development gap exists between core regions and peripheral cities, which manifests as fragmented industrial linkages and inadequate intercity integration. The degree of regional economic path divergence surpasses typical convergence patterns. Coordinated economic development has emerged as a notable challenge requiring urgent attention in the GBA. This situation indicates a need for targeted policy interventions to promote collaborative development. In response to issues identified in the study, this paper puts forward several policy suggestions, such as establishing a coordinated mechanism for regional economic development, in order to promote coordinated development of the economy, aiming to provide data support and a policy basis for further development.</p>