Under the special institutional environment of “One country, Two systems, and Three jurisdictions” in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), cross-border trade finance faces prominent information asymmetry and institutional frictions. Existing studies lack quantitative evaluation of blockchain technology’s application efficiency in this context and systematic analysis of barrier mechanisms. This paper constructs an analytical framework of “technological characteristics-financing process-efficiency output”, using the DEA-BCC model, Malmquist index, grounded theory, and ISM-ANP model for empirical analysis. The results showed that blockchain significantly empowers cross-border trade finance, with total factor productivity (TFP) increasing by 14% in 2023–2024, mainly driven by technological efficiency improvement. Core enterprises (comprehensive technical efficiency 0.82) outperform SMEs (0.65), showing a “Matthew Effect”. Moreover, barriers form a three-level structure of “underlying root-middle-level transmission-surface manifestations”, with technical (weight 0.32) and institutional barriers (0.28) as core constraints, especially insufficient cross-border regulatory coordination (0.12) and inconsistent cross-chain standards (0.10). Prioritizing these underlying barriers is key to breaking “digital silos”, and the proposed hierarchical governance strategy provides support for GBA financial infrastructure interconnection.