The invention discloses material composition of a halogen-free printed circuit board with low dielectric loss and a manufacturing method thereof, which are applied to the manufacturing environment ofa substrate material of the printed circuit board. The material composition of the halogen-free printed circuit board with the low dielectric loss mainly comprises a phosphor-containing phenolic resintaken as a crosslinking agent; and the crosslinking agent can make the substrate material of the printed circuit board pass a UL 94-0 flame retardant test, can also make phosphor combined with the material into a material structure to eliminate the worry of precipitation, and can be matched with a resin with low dielectric loss characteristic and inorganic powder so as to reduce the dielectric constant and the dielectric loss of the material. The material composition of the halogen-free printed circuit board with the low dielectric loss has the advantages of low dielectric loss characteristic, heat resistance and low expansibility, and can also meet the requirement of no lead solder to meet the requirements of the market and environmental protection at the same time.