Huntington’s disease (HD) is an autosomal dominant neurodegenerative disease caused by the mutational expansion of CAG triplet repeat in mutant Huntingtin (mHTT) protein. These proteins form aggregates in the affected neurons of patient brains that correlate with disease progression and toxicity. Recent studies reported chaperone can prevent protein misfolding and serve as powerful inhibitor mutant HTT-induced neurotoxicity. According to the recent studies, FKBP12 chaperone had PPIase activity and be decreased the protein level in HD mouse. Another chaperone, Trigger factor (TF), the TFPPIase and FKBP12 are structural homology, can decrease protein aggregates. Here, we investigated whether the presence of FKBP12/TF chaperone could effectively change amounts and properties of polyQ aggregates by biophysical/biochemical technique. We have successfully established the GST-polyQ system and apply in vitro aggregation assay to unravel the effect of chaperone in aggregation process. Turbidity assay and filter assay revealed TF can significantly suppress HTT43Q aggregates, while FKBP12 increase HTT43Q aggregates. Moreover, we examined the morphology of HTT25Q and HTT43Q in the presence/absence of TF/FKBP12 under Transmission Electron Microscopy (TEM). Massive fibrils can be observed in HTT43Q only. To our surprise, TF significantly changed the morphology of HTT43Q and formed short protofibril structures. Meanwhile, FKBP12 formed amorphous aggregate structures. We further used Thioflavin T (ThT) fluorescence to detect amyloidogenic fibrils. Results showed that TF can FKBP12 can both suppress amyloid fiber at day 1. The inhibition effect can still be seen in FKBP12 but not in TF at day 7, indicating TF can only retard the amyloidogenic process while FKBP12 can shift the process to form non-amyloid aggregates. From the FT-Raman spectroscopy,β-sheet composition both decreased in TF and FKBP12 compared with HTT43Q only. Here, we propose TF and FKBP12 can modulate mHTT protein aggregation in different pathway. While TF can only retard the amyloidogenic process, FKBP12 can shift the process to form non-amyloid aggregates. This may shed light on the future therapeutical treatments of Huntington’s disease.