The invention relates to electron beam machining energy control method which is used in materials processing. According to the distributing demand of the energy density at the work piece, the number of the scanning point in each position of the scanning trace is distributed or the flow value of the electron beam is controlled, or both of the methods are adopted at the same time to control the energy density of the heated work piece surface. Then the required energy density distribution is gained at the surface of the heated work piece. Heterogeneous metal are welded by respectively controlling the amount of the scanning point at the both sides of the joint, the distribution of the scanning point, and the flow value of the electron beam to control the energy input at the both sides of the joint, so that the molten charge of the heterogeneous metal is adjusted at the both sides of the joint. The invention realizes the energy density control at the different position of the scanning trace, can respectively practice energy density control to each scanning trace at the condition that the scanning traces are many, and can effectively control the molten charge of the heterogeneous metal at the both sides of the joint while welding the heterogeneous metal.