High-speed (HS) atomic force microscopy (AFM) is a prominent imaging technology that observes large-scale structural dynamics of biomolecules near the physiological condition, but the AFM data are limited to the surface shape of specimens. Rigid-body fitting methods were developed to obtain molecular structures that fit to an AFM image, without accounting for conformational changes. Here we developed a method to fit flexibly a three-dimensional biomolecular structure into an AFM image. First, we describe a method to produce a pseudo-AFM image from a given three-dimensional structure in a differentiable form. Then, using a correlation function between the experimental AFM image and the computational pseudo-AFM image, we developed a flexible fitting molecular dynamics (MD) simulation method, by which we obtain protein structures that well fit to the given AFM image. We first test it with a twin-experiment; using an AFM image produced from a protein structure different from its native conformation as a reference, we performed the flexible fitting MD simulations to sample conformations that fit well the reference AFM image, and the method was confirmed to work well. Then, parameter dependence in the protocol was discussed. Finally, we applied the method to a real experimental HS-AFM image for a flagellar protein FlhA, demonstrating its applicability. We also test the rigid-body fitting of a molecular structure to an AFM image. Our method will be a general tool for dynamic structure modeling based on HS-AFM images and is publicly available through CafeMol software.