Transition-metal-doped Bi2Se3 crystals, X0.05Bi2Se3 (X = Cr, Co, Ni, and Cu), are prepared and studied by powder x-ray diffraction and extended x-ray absorption fine structure (EXAFS) measurements to get the local structures around the dopants. Cr atoms substitute Bi atoms and Co atoms may substitute Bi atoms or form Co3Se4 (C2/m) clusters. Cu is also found taking the Bi substitutional site, which differs from the reported superconductor phase of Cu-doped Bi2Se3, suggesting the dependence of site occupancy of Cu in Bi2Se3 on the process of sample growing. For Ni0.05Bi2Se3, Ni atoms form Ni3Se4 (C2/m) clusters. The nearest neighbors of X (X = Cr, Co, and Cu) are Se atoms, and the X-Se bond lengths are extracted from EXAFS as 2.50 angstrom for Cr-Se, 2.40 angstrom for Co-Se, and 2.38 angstrom for Cu-Se, which show the direct evidences of dramatic structural relaxations around 3d dopants. The bond information of local structures around dopants is valuable for subsequent theoretical studies, and can hardly be obtained from other techniques.