We performed X-ray fluorescence holography measurements on a single crystal Mg85Zn6Y9 alloy, having a synchronized 18R long period stacking ordered structure, and successfully obtained Zn Kα holograms. The reconstruction shows “U”-shaped atomic images in remarkable contrast to the prediction of an existing model with Zn6Y8 L12 clusters. To explain this feature we calculated holograms using a model with positional fluctuations, and fit the reconstruction to the experimental results. It was found that large rotational fluctuations of the clusters can explain the “U”-shaped images.