The Centiloid (CL) is a method for standardizing amyloid beta (Aβ) quantification through different ligands and methods. To find the most appropriate reference region to reduce the variance in the Aβ CL unit between 18F-florbetaben (FBB) and 18F-flutemetamol (FMM), we conducted head-to-head comparisons from 56 participants using the direct comparison of FBB-FMM CL (dcCL) method with four reference regions: cerebellar gray (CG), whole cerebellum (WC), WC with brainstem (WC + B), and pons. The FBB and FMM dcCL units were highly correlated in four reference regions: WC (R2 = 0.97), WC + B (R2 = 0.98), CG (R2 = 0.92), and pons (R2 = 0.98). WC showed the largest effect size in both FBB and FMM. Comparison of the variance of the dcCL values within the young control group showed that with FBB, WC + B had the smallest variance and with FMM, the WC had the smallest variance. Additionally, WC + B showed the smallest absolute difference between FBB and FMM, followed by the WC, pons, and CG. We found that it would be reasonable to use the WC or WC + B as the reference region when converting FBB and FMM SUVRs into dcCL, which can increase the accuracy of standardizing FBB and FMM PET results.