The aggregation behavior of thermoresponsive polyelectrolytes with low charge density in aqueous solutions of organic counterions was investigated. We synthesized two thermoresponsive polyelectrolytes: anionic poly(N-isopropylacrylamide-co-(3-sulfopropyl)acrylamide potassium) (P-NIP-SPAK) and cationic poly(N-isopropylacrylamide-co-(3-acrylamidepropyl)trimethylammonium chloride) (P-NIP-AAPTAC). The polyelectrolytes remained soluble in their aqueous solutions even above the lower critical soluble temperature of P-NIP owing to the strong hydration property of the ionic groups. The aggregation occurred when organic counterions were added to the solution. In these solution systems, the concentration of counterions exceeds those of ionic groups introduced into the polyelectrolytes. The aggregation behavior is attributed to the salting-out effect of counterions accommodated near the polyelectrolyte surface by electrostatic interaction. This aggregation behavior was utilized for the charge-selective recognition of amino acids. P-NIP-SPAK aggregated only when basic amino acids were added under acidic conditions, whereas P-NIP-AAPTAC aggregated only when acidic amino acids were added under basic conditions. The results herein demonstrate that P-NIP-SPAK and P-NIP-AAPTAC have the potential to be used as charge-selective polymer sensors for amino acids without having to strictly control the experimental conditions.