The phase shift of light or electrons in objects is now necessary for probing weak-phase objects such as unstained biological specimens. Optical microscopy (OM) and transmission electron microscopy (TEM) have been used to observe weak-phase objects. However, conventional OM has low spatial resolution and TEM is limited to thin specimens. Here, we report on the development of dark-field X-ray ptychography, which combines X-ray ptychography and X-ray in-line holography, to observe weak-phase objects with a phase resolution better than 0.01 rad, a spatial resolution better than 15 nm, and a field of view larger than 5 μm. We apply this method to the observation of both the outline and magnetosomes of the magnetotactic bacteria MO-1. Observation of thick samples with high resolution is expected to find broad applications in not only biology but also materials science.