Kanamycin (KANA) plays a key role in the treatment of bacterial infections and has been widely used in animal husbandry. However, its overuse causes antibiotic residues in animal-derived foods. Determination methods for KANA are urgently needed for food safety. Most of the developed fluorescent aptamer sensors for detecting KANA use parental aptamer (kana-Apt) as recognition unit. However, excessive bases tend to form secondary structures and lead to high background or nonspecific signals. In this study, two fluorescent sensors based on one (kana1-Apt) and two (kana1/kana2-Apt) split fragments were developed for KANA detection. The LODs of the kana1-Apt/ThT system and kana1/kana2-Apt/ThT systems were 4.88 nM and 4.53 nM, respectively. In addition, satisfactory recoveries of the kana1-Apt/ThT system and kana1/kana2-Apt/ThT system were obtained in the detection of KANA in milk, which were 97.6%-104.5% and 98.4%-105.9%, respectively. Moreover, the results indicated that the kana1-Apt fragment plays a critical role in recognition. In conclusion, the results of the present study provide a novel strategy for molecular detection based on split aptamers.