The fluorescence of conjugated polyelectrolytes (CPEs) is efficiently quenched by low concentrations of quenchers with opposite charges. We have reported the close correlation between this amplified quenching phenomenon and CPE chain aggregation. In this paper, we further demonstrate the profound correlation between the fluorescence quenching efficiency, CPE chain aggregation, and quencher molecular size. Aggregation of a poly(phenylene ethynylene)-type CPE (PPE-CO2-) is induced by the addition of either water or Ca2+ to methanol solution, as indicated by absorption, fluorescence, dynamic light scattering, and fluorescence microscope measurements. For quencher ions with a small molecular size, such as methyl viologen (MV2+), either the loose (induced by the addition of Ca2+) or the compact (induced by the addition of water) CPE chain aggregates are beneficial to the fluorescence quenching. For quencher ions with large molecular size, such as tris(4,7-diphenyl-1,10-phenanthroline)ruthenium (Ru(dpp)(3)(2+)), however, the loose chain aggregates are found to be favorable for quenching, while the quenching efficiency is lower for the compact polymer aggregates present in aqueous solution.