Abstract: Innovation synergy in cross-boundary regions is a necessary step toward deep regional integration and an indispensable component of regional innovation networks. Compared with the one-way pull of the "core-periphery" model, the multidirectional "periphery-periphery" linkages in cross-boundary regions offer a key way to understand how their innovation-synergy patterns take shape. From a potential difference perspective, this paper explains the mechanism of innovation synergy in cross-boundary regions. It first clarifies the meaning of potential-difference coupling and the matching mechanism among three structural phases - endowment, efficiency and environment - and then develops a four- quadrant framework of innovation synergy under the logic of potential difference. Two typical spatial organization models are identified: multidirectional linkage and balanced interaction. Using the Shanghai-Suzhou-Jiaxing cross-boundary region as an empirical case, the paper identifies a development pattern of "salient potential differences and differentiated phases" and a synergy condition of "broad connectivity but weak stability". It verifies the proposed mechanism and then proposes a guidance framework of "proximity-based complementarity plus network linkage" and a leapfrogging path from "absence" to "emergence", "optimization" and "refinement". The study provides theoretical and empirical references for addressing innovation-synergy dilemmas in cross-boundary regions.