Anti-idiotypic nanobodies, usually expressed by gene engineering protocol, has been shown as a nontoxic coating antigen for toxic compound immunoassays. We here focused on how to increase immunoassay sensitivity by changing the nanobody's primary sequence. In the experiments, two anti-idiotype nanobodies against monoclonal antibody 1H2, which is specific to ochratoxin A, were obtained and named as nontoxic coating antigen 1 (NCA1) and nontoxic coating antigen 2 (NCA2). Three differences between the nanobodies were discovered. First, there are six amino acid residues (AAR) of changes in the complementarity determining region (CDR), which compose the antigen-binding site. One of them locates in CDR1 (I-L), two of them in CDR2 (G-D, E-K), and three of them in CDR3 (Y-H, Y-W). Second, the affinity constant of NCA1 was tested as 1.20 × 10 8 L mol −1 , which is about 4 times lower than that of NCA2 (5.36 × 10 8 L mol −1 ). Third, the sensitivity (50% inhibition concentration) of NCA1 for OTA was shown as 0.052 ng mL −1 , which was 3.5 times lower than that of nontoxic coating antigen 2 (0.015 ng mL −1 ). The results indicate that the AAR changes in CDR of the anti-idiotypic nanobodies, from nonpolar to polar, increasing the affinity constant may enhance the immunoassay sensitivity. In addition, by using the nontoxic coating antigen 2 to substitute the routine synthetic toxic antigen, we established an eco-friendly and green enzyme-linked immunosorbent assay (ELISA) method for rapid detection of ochratoxin A in cereals. The half-maximal inhibitory concentration (IC 50 ) of optimized ELISA was 0.017 ng mL −1 with a limit of detection (LOD) of 0.003 ng mL −1 . The optimized immunoassay showed that the average recoveries of spiked corn, rice, and wheat were between 80% and 114.8%, with the relative standard deviation (RSD) ranging from 3.1-12.3%. Therefore, we provided not only basic knowledge on how to improve the structure of anti-idiotype nanobody for increasing assay sensitivity, but also an available eco-friendly ELISA for ochratoxin A in cereals.Key Contribution: Two anti-idiotype nanobodies were developed and used as non-toxic antigens against monoclonal antibody 1H2, which is specific to ochratoxin A. A basic knowledge was discovered Toxins 2020, 12, 273 2 of 15 that the change of amino acid residues in idiotypic nanobodies enhanced the sensitivity by comparing the amino acid sequences, structure, affinity constants, and sensitivities between both nanobodies.