A novel phosphorus-containing compound (DOPO-THPO) is synthesized via the Atherton-Todd-reaction between 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) and trihydroxymethylphosphine oxide (THPO), and then employed as flame retardant for diglycidyl ether of bisphenol A/4-4 diaminodiphenylmethane epoxy resin (DGEBA/DDM). Based on the ultra-low phosphorus loading, the highly efficient flame retarded epoxy resin (EP) systems are successfully established in this work. Remarkable improvements in the limited oxygen index (LOI) values and UL-94 rating of flame retarded EP systems are observed. In detail, when the phosphorus content is only 0.33 wt%, the EP composite receives V-0 rating in the UL-94 vertical burning test with LOI value of 30%. Heat release of EP composites is obviously inhibited with the formation of intumescent char residue. Furthermore, TG-IR result of DOPO-THPO shows the generation of phosphorus containing products, which may provide a gaseous phase flame retardant function on EP. This work may open the new door for the construction of highly efficient flame retardant EP system based on the ultra-low phosphorus loading.