Two cationic poly(fluorene-alt-benzothiadiazole)s with different side chains are designed and synthesized. Both polymers show low fluorescence in aqueous solution due to the charge-transfer character of the polymer's excited states. Fluorescence turn-on biosensors for heparin detection and quantification are developed, taking advantage of complexation-induced aggregation, which increases the polymer fluorescence in aqueous solution. It is found that good polymer water-solubility is beneficial to the sensitivity and fluorescence contrast of the heparin turn-on sensor as a result of the low fluorescence background. Moreover, stronger complexation between the polymer/heparin leads to a substantially larger fluorescence increase in the presence of heparin relative to that in the presence of its analog, hyaluronic acid (HA), allowing discrimination of heparin from HA. Heparin quantification with a practical calibration range covering the whole therapeutic dosing levels (0.2-8 U mL(-1)) is realized based on the polymer with good water-solubility. This investigation provides a new insight for designing conjugated polymers with a light-up signature for biomolecular sensing.