The invention belongs to the technical field of copper clad laminate production, and particularly relates to a manufacturing method of a halogen-free, phosphorus-free, environment-friendly and flame-retardant paper-based copper clad laminate. Brand-new nitrogen-containing phenolic resin is used in cooperation with other fillers, so that the flame retardancy, machinability and other basic performance of the copper clad laminate are ensured. In the manufactured copper clad laminate manufactured by the invention, the halogen content of chlorine is less than or equal to 0.09 percent, the content of bromine is less than or equal to 0.09 percent, and or the total content of the chlorine and the bromine is less than or equal to 0.15 percent, thereby meeting the requirement of freeness from halogen; moreover, no phosphorus-containing compound is added, and the phosphorus content is less than or equal to 0.1 percent. The flame retardancy of the manufactured copper clad laminate meets the FV0 grade requirement, the cost is lowered, and the heat resistance is enhanced greatly; the copper clad laminate is halogen-free, phosphorus-free and environment-friendly.