The recently prepared CrI3/WSe2 heterostructure has attracted considerable attention, understanding the in-fluence of structural defects on the magnetic and electronic properties of CrI3/WSe2 heterostructure is of great significance for its practical application. In this paper, we systematically investigate the effect of 3d transition metal (TM) atoms (TM = Sc, Ti, V, Mn, Fe, Co, Ni, Cu and Zn) intercalation on the structural, electronic and magnetic properties of CrI3/WSe2 heterostructure based on first-principles calculations. The most stable inter-calation site is TW1 for Sc, Ti, V, Mn, Fe and Co atoms embedded systems, and TSe2 for Ni, Cu and Zn atoms embedded systems. TM atoms enhance the total magnetic moment of CrI3/WSe2 heterostructure. Except for Ti atom, the other TM atoms switch the easy axis of CrI3/WSe2 heterostructure from out-of-plane to in-plane di-rection. The intercalation of TM atoms can enhance the ferromagnetic stability of CrI3/WSe2 heterostructure depending on the embedded TM atoms. CrI3/WSe2 heterostructures intercalated with TM atoms exhibit half-metallic state. These results may provide an efficient approach to tune the property of CrI3/WSe2 hetero-structure and prepare it better for the application in spintronic devices.