Amyloid fibrils have been highlighted due to their pathological role, which is determined by their conformations. For instance, the conformations of prion amyloid fibrils determine the prion infectivity. Despite recent findings regarding the important role of the conformational diversity of amyloid fibrils in their pathological role, the underlying mechanisms in amyloid fibril formation with conformational heterogeneity have remained elusive. In this work, we employed the microwave-based chemical synthesis which allows us to finely tune the thermodynamics of self-assembly process leading to the conformational diversity of amyloid fibrils. It is shown that the length of amyloid fibril and the helical structure of the fibril can be controlled using microwave irradiation. This study sheds light on the microwave-based chemical synthesis for studying the conformational heterogeneity of amyloid fibrils and for developing novel design protocol, which allows for delicately manipulating the molecular structure of protein fibrils.