In-depth studies of the two types of Te nanoprecipitates, linear and elliptic, in Cd1–xZnxTe (CZT) crystals grown by a modified vertical Bridgman method have been carried out. Electron diffraction suggests that linear Te nanoprecipitates align their Te atoms in a similar way to CZT structure, while elliptic Te nanoprecipitates cluster Te atoms following the pure trigonal Te structure. The three-dimensional morphology for both linear and elliptic Te nanoprecipitates has been revealed by delicate energy-dispersive x-ray analysis under electron microscopy. The density of elliptic Te nanoprecipitates ranges from 1015 to 1017 cm−3, while linear ones usually several times lower for a certain CZT wafer. The origin of both types of Te nanoprecipitates has been discussed in terms of the local density of intrinsic point defects in CZT. CZT properties are influenced more negatively by elliptic Te nanoprecipitates, which shed light on the methodology for crystal growth: preventing the clustering of intrinsic point defects during the crystal growth will be essential to obtain high quality CZT crystal.