Diagrid system has received increasing attention by designers and researchers of high-rise building. In this paper, an innovative super high-rise diagonal mega frame-core tube structure adopting topology optimization for two-dimensional diagrid mesh and shape optimization for three-dimensional outline was introduced. Different from traditional diagrid structures, eight corner columns and a number of corner beams were used in the external diagrid frame, leading to unique spatial working capacity. In order to assess and study the seismic performance of this innovative structure, a series of shaking table tests on a 1/35 scaled model were conducted. Three earthquake waves and three seismic intensity levels were considered during the tests and the external diagrid frame tube showed strong lateral stiffness while severe tensile damage occurred at the bottom of corner columns under maximum considered earthquakes. Then repair work of the test model was initiated and second part of shake table test was conducted which covered the same loading steps of the first part test and more loading steps of two higher seismic levels. Based on a large amount of test data recorded, the acceleration response, displacement response, strain response, seismic fragility and hysteretic energy dissipation of this structure were analyzed. This structure performed satisfactory seismic performance and collapse resistance capacity without obvious whiplash effect and weak story. Corner columns became the key components due to their tremendous axial forces and welding connections of corner columns became the comparatively weak parts in this system, which need be carefully concerned in practical project.