The invention provides a flax half bleached yarn manufacturing method with dyeing differentiation. The method comprises: dividing flax roving into two groups, using two different chemical treatment processes to treat, and then feeding the flax roving obtained after the two different chemical treatment processes into a drafting region of spun yarns, through drafting, twisting to spin a single yarn, similar to siro spinning, finally drying and spooling and forming, to manufacture a flax half bleached yarn with dyeing differentiation. After the spun flax half bleached yarn with dyeing differentiation is dyed, the yarn has color spun style, but evenness, strength, and yarn hairness are superior to evenness, strength, and yarn hairness of a flax long ramie color spun yarn. The manufacturing process is shorter than technological process of a color spun yarn. The method is low in manufacturing cost and good in spinnability. The novel differentiation linen expands and enriches kinds of flax yarn products, and is suitable for yarn dyeing and grey dyeing, and has good weaving selectivity. Fabric styles are unique, and the flax half bleached yarn has good market competitiveness and good market prospect.