Different levels of institutional quality have different effects on the agglomeration of innovative elements，driving different forms of agglomeration of innovative elements，and affecting the high-end industrial structure. This paper constructs an endogenous growth model with the addition of a spatial weight matrix to analyze the issue of institutional choice in the process of high-end industrial structure，and then empirically explores the space where the concentration of innovative elements at all levels within the three spatial thresholds of institutional quality drives the high-end industrial structure of our country action effect. The study found that the quality of the system within the three spatial thresholds contributed to the agglomeration of elementary，intermediate and advanced innovative elements. The spatial effect of the concentration of innovative elements on the high-end industrial structure is directly proportional to the degree of institutional quality，and the spatial effect of technology spillovers on the high-end industrial structure is inversely proportional to the degree of institutional quality. The effect of institutional quality in driving the high-end industrial structure driven by the agglomeration of innovative elements decreases as the level of agglomeration of innovative elements increases. Only when the quality of the regional system and the level of agglomeration of innovative elements are consistent，and then adopting corresponding forms of technological innovation can the industrial structure be advanced.