PET-based Alzheimer's disease (AD) assessment has many limitations in large-scale screening. Non-invasive techniques such as resting-state functional magnetic resonance imaging (rs-fMRI) have been proven valuable in early AD diagnosis. This study investigated feasibility of using rs-fMRI, especially functional connectivity (FC), for individualized assessment of brain amyloid-β deposition derived from PET. We designed a graph convolutional networks (GCNs) and random forest (RF) based integrated framework for using rs-fMRI-derived multi-level FC networks to predict amyloid-β PET patterns with the OASIS-3 (N = 258) and ADNI-2 (N = 291) datasets. Our method achieved satisfactory accuracy not only in Aβ-PET grade classification (for negative, intermediate, and positive grades, with accuracy in the three-class classification as 62.8% and 64.3% on two datasets, respectively), but also in prediction of whole-brain region-level Aβ-PET standard uptake value ratios (SUVRs) (with the mean square errors as 0.039 and 0.074 for two datasets, respectively). Model interpretability examination also revealed the contributive role of the limbic network. This study demonstrated high feasibility and reproducibility of using low-cost, more accessible magnetic resonance imaging (MRI) to approximate PET-based diagnosis.