To realize the separation of phenanthrene from anthracene residue efficiently, a reaction–separation coupling technology was adopt by converting fluorene to its valuable derivative, and then phenanthrene was isolated according their solubility difference. The effect of solvents, feeding sequence and the material ratios on the synthesis of 9,9-bis(hydroxymethyl)fluorene by one-step hydroxymethylation of fluorene was investigated firstly, and then the reaction–separation process conducted with a mixture of phenanthrene and fluorene at a mass ratio of 4:1. The result showed that adding fluorene into alkaline formaldehyde solution can improve the selectivity of 9,9-bis(hydroxymethyl)fluorene, and with the mixture of DMSO and ethanol as solvent, the highest yield of 84.24% is obtained by using anhydrous potassium carbonate as base catalyst. The reaction applied for the mixture of phenanthrene and fluorene, the purity of 9,9-bis(hydroxymethyl)fluorene of 87.26% was obtained with a yield of 73.87%, and the yield of phenanthrene is 98.96% with a purity of 97.18%.