Small three-photon absorption (3PA) cross-section values of present nonlinear organic molecules limit their practical applications. Although electron donors and electron acceptors have a great effect on 3PA cross-section, little is known about how the strength and situation of electron acceptors influence the 3PA cross-section value of a compound. The present work reports 3PA effects of two fluorene derivatives with symmetric D-π-π(A)-π-D archetype, which are named as 2,7-bis(4-methoxyphenylacetylene)-9-fluorenone (FATT) and 2,7-bis(4-methoxyphenylacetylene)-9-thoine-fluorene (TSATL). Large 3PA cross-section and ideal 3PA-induced optical limiting effects have been found in the two fluorene derivatives. The two molecules both have a different electron acceptor on the fluorene core, by which the 3PA cross-section value for FATT is enhanced by nearly 3-fold compared with that for TSATL. The mechanism of this significant enhancement in 3PA cross-section has been investigated by density functional theory (DFT) and configuration interaction singles (CIS) method with use of 6-311+G basis set in combination with conductor polarizable continuum model (CPCM). The theoretical results show that increase of electronegative character of the electron acceptor on the core is responsible for the increase of 3PA cross-section values of the two molecules.