The embodiment of the invention provides a crop canopy in-situ growth phenotype monitoring device and a three-dimensional reconstruction method. Through a data acquisition and collection module arranged on a canopy top, an image acquisition module arranged in a canopy, and a fisheye lens arranged on a canopy bottom, the morphological structure data of the top, the interior and the bottom of the canopy of the crop to be detected can be obtained, and the height and the angle of the image obtaining module in the canopy can be adjusted, so that the morphological structure data in the canopy are richer, and finally, the growth monitoring of the canopy of the crop to be monitored is more accurate and overall, and the universality is very good. The canopy growth monitoring device is used for obtaining the morphological structure data of the top, the interior and the bottom of the canopy, the morphological structure data are used for phenotypic analysis and three-dimensional reconstruction after certain pretreatment, the workload is small, the efficiency is high, and the obtained three-dimensional reconstruction model is high in precision.