The invention discloses an integrated circuit structure with semiconductor elements, and a manufacturing method of the integrated circuit structure. The integrated circuit structure comprises a substrate, a plurality of semiconductor elements and an ultra-deep trench isolation structure, wherein the substrate has opposite top surface and bottom surface, and comprises multiple regions; the multiplesemiconductor elements are formed on the substrate and positioned in different regions; and the ultra-deep trench isolation structure is formed in the substrate and surrounds each region so as to isolate the semiconductor elements positioned in different regions, wherein the ultra-deep trench isolation structure extends from the top surface to the bottom surface of the substrate to pass through the substrate.