Streptococcus suis, a significant zoonotic pathogen, annually caused substantial economic losses in the swine industry and had intensified threat to public health due to the recent emergence of human-associated clade. In this study, we discovered that the rare-earth metal-based metal-organic frameworks (Y-BTC) possessed excellent ECL capabilities. After prereduction at high voltage, its ECL intensity was enhanced by two times. Subsequently, we developed an efficient CRISPR/Cas12a-mediated electrochemiluminescence resonance energy transfer (ECL-RET) biosensor utilizing Y-BTC for the detection of the human-associated S. suis clade. Y-BTC was employed as the ECL-RET donor and ECL emitter, and the spherical nucleic acid Au NP was utilized as the ECL-RET receptor. In the presence of the target, isothermal amplification was triggered to generate a large number of amplicons, which subsequently activated the trans-cleavage activity of Cas12a. Cas12a cleaved the nucleic acid shell on the surface of Au NPs, reducing the spatial distance between Au NPs and Y-BTC due to electrostatic adsorption, thereby quenching the ECL of Y-BTC via ECL-RET. Consequently, the presence of targets can be observed by a reduced ECL signal. The sensor exhibited a detection range of 25 pM to 50 nM, with a detection limit as low as 17 pM. The practical utility was verified through actual sample testing. Our proposed ECL-RET sensing strategy provides a new avenue for the sensitive detection of S. suis. The universality has also been demonstrated using Fusobacterium nucleatum, Salmonella pullorum, and Listeria monocytogenes, holding great promise in the field of food safety and public health.