We report the design and synthesis of two pyrimidine-functionalized charge transfer probes and their host-guest interactions with cyclodextrins (CDs), focusing on β-CD and its nanosponge (NS) derivative. One probe, featuring extended conjugation, exhibited aggregation-induced quenching in water but showed ∼2.3-fold fluorescence enhancement with a ∼3 nm blue shift upon β-CD complexation, indicating effective encapsulation and consequent disaggregation. Time-dependent studies revealed a ∼15-18 min kinetic window for effective complexation, whereas fluorescence anisotropy increased from 0.14 to 0.32, confirming the restriction of the overall molecular reorientation. Job's plot and a binding constant of 6866 M-1 supported a 1:1 inclusion complex. The β-CD NS (nanosponge) further enhanced the emission (∼8.9-fold after incubation), outperforming native β-CD. In contrast, the other probe, with a shorter conjugation length, displayed poor binding interactions with β-CD. Computational and docking studies supported the experimental findings, revealing favorable cavity-compatible binding interactions in the case of the longer-conjugated system. The probe also exhibited a selective turn-on fluorescence response to the cyanide anion (-CN) (∼4.1-fold) in the β-CD complex. The presence of β-CD enhanced the binding affinity for -CN through multiple polar contacts and additional hydrogen bonding interactions. This work offers a promising strategy for the aqueous-phase sensing of toxic anions by using supramolecular assemblies.