Two types of isomeric bi‐DOPO(9,10‐dihydro‐9‐oxa‐10‐phosphaphenan threne‐10‐oxide) flame retardants named DHK(6,6’‐((4,6’‐dihydroxy‐[1,1’‐biphenyl]‐3,3’‐diyl)bis(propane‐3,1‐diyl))bis(dibenzo[c,e][1,2] oxaphosphinine 6‐oxide)) and DMG (6,6’‐((6,6’‐dihydroxy‐[1,1’‐biphenyl]‐3,3’‐diyl) bis (propane‐3,1‐diyl)) bis (dibenzo [c,e][1,2] oxaphosphinine 6‐oxide)) are successfully prepared and their flame retardant properties are investigated. Although they have the same phosphorus content, the corresponding thermoset DHK/Epoxy resins (EP) and DMG/EP show different flame retardancy. The flame retardant mechanism is compared by thermal analysis coupled with Fourier transform infrared (TG‐FTIR), residue FTIR, elemental analysis, Raman spectra, scanning electron microscopy (SEM), and cone calorimetry. More phosphorus remains in the residue of DHK/EP which suggests better‐condensed phase flame retardancy than that of DMG/EP. However, DMG shows a better flame inhibition effect than that of DHK. The results of mean square displacement, free volume fraction, and cohesive energy density in molecular dynamics simulations show that the weakening of the movement ability of the DMG/EP molecular segments should be the reason for the increase in toughness. This shows that although flame retardants possess the same composition, their structure will also affect their flame retardant mechanism and properties, which provide a guide for the design and preparation of high‐efficiency flame retardants.