Ion probe zircon U-Pb dating has been widely used in earth and planetary sciences research. Previous studies found that ion probes have problems in the U-Pb dating of zircon with high U content. When the U content of zircon reaches a high threshold, the apparent age of U-Pb will become scattered and mostly older, which is called the “high U effect”. Based on micron-scale observations, predecessors have proposed that the spontaneous alpha decay of high content of radioactive element U and its daughter nuclear recoil will damage the zircon lattice, resulting in an increased yield of Pb+ in SIMS analyses and therefore an older 206Pb/238U age. However, there are also studies showing that zircons that have not been damaged also show a “high U effect”. In this contribution, scanning electron microscopy, ion probe and atom probe tomography research were carried out on high U content zircon grains (3.0 ± 0.1 Ma) in a highly fractionated leucogranites from the Himalayas to study the microcosmic occurrence state of zirconium constituent elements. Results show that these zircon grains have extremely high U contents ranging from 4271 to 95,176 μg/g. The distribution of U, P and Y in zircon is inhomogeneous, with enrichment features in local nanoscale regions. Zr constituent elements mainly exist in two states: (1) lamellar enrichment region, which corresponds to the compositional oscillation ring of zircon. The lamellar high U region is nearly parallel distributed. Its composition is in the transition between zircon, coffinite (USiO4) and xenotime; (2) The agglomerated high U region, which appears as isolated particles in zircon with a composition close to coffinite. The composition of the observed highest U region is Zr2.7Si12.2O61.8U19.8P1.4Y1.2Yb0.6Hf0.3, and the particle size is ∼8 nm. Nanoscale coffinites and xenotimes in high U zircons result in obvious differences between the matrix with the ion probe zircon standard reference materials, which resulted in the “high U effect”.