We performed a TMT-based proteomic study of dikaryon and the two compatible monokaryons to probe the profiles of different biological processes and their coordination that contribute to the dikaryon growth advantage. Results suggested diverse processes respond to the dikaryon and coordination of these processes contribute to the dikaryon growth advantage, especially the transfer from energy metabolism to biosynthesis and growth with high energy utilization efficiency. This will be favourable for breeding of Ganoderma lucidum.