Circadian rhythms are closely associated with human health, and the detection of relevant markers is essential to avoid circadian disorders. Here, we report a biosensing platform based on aggregation-induced emission for the sensitive detection of such markers. In this platform, the structure of 4,4',4″,4‴-(ethene-1,1,2,2-tetrayl)tetrabenzaldehyde (ETBA) was modulated at the molecular level to 4',4‴,4‴″,4⁗‴-(ethene-1,1,2,2-tetrayl)tetrakis([1,1'-biphenyl]-4-carbaldehyde) (ETBCA), thereby increasing the energy levels of the highest and lowest unoccupied molecular orbitals, reducing the energy gap, and enhancing the conjugation effect, ultimately improving the fluorescence properties of the molecule. ETBCA was the starting monomer used to synthesize ETBCA-loaded nanoparticles (ETBCANPs) with higher quantum yields and longer fluorescence lifetimes, which were then loaded onto responsive DNA hydrogels for the sensitive detection of melatonin. The resulting loaded hydrogel (ETBCANPs@Hydrogel) showed superior performance compared to hydrogels loaded with ETBA nanoparticles and quantum dots, with 2.9- and 3.6-fold higher sensitivities, respectively. The ETBCANPs@Hydrogel was able to detect melatonin in saliva and urine samples with limits of detection of 18.6 pg/mL and 10.5 pg/mL, respectively, recoveries of 94.2-107.5%, and satisfactory selectivity. In summary, the fluorescence performance of aggregation-induced emission molecules can be effectively improved by modulating their molecular structure, leading to the development of hydrogels for the sensitive sensing and detection of circadian rhythm disorders.