As global temperatures warm, drought reduces plant yields and is one of the most serious abiotic stresses causing plant losses. The early identification of plant drought is of great significance for making improvement decisions in advance. Chlorophyll is closely related to plant photosynthesis and nutritional status. By tracking the changes in chlorophyll between plant strains, we can identify the impact of drought on a plant’s physiological status, efficiently adjust the plant’s ecosystem adaptability, and achieve optimization of planting management strategies and resource utilization efficiency. Plant three-dimensional reconstruction and three-dimensional character description are current research hot spots in the development of phenomics, which can three-dimensionally reveal the impact of drought on plant structure and physiological phenotypes. This article obtains visible light multi-view images of four poplar varieties before and after drought. Machine learning algorithms were used to establish the regression models between color vegetation indices and chlorophyll content. The model, based on the partial least squares regression (PLSR), reached the best performance, with an R2 of 0.711. The SFM-MVS algorithm was used to reconstruct the plant’s three-dimensional point cloud and perform color correction, point cloud noise reduction, and morphological calibration. The trained PLSR chlorophyll prediction model was combined with the point cloud color information, and the point cloud color was re-rendered to achieve three-dimensional digitization of plant chlorophyll content. Experimental research found that under natural growth conditions, the chlorophyll content of poplar trees showed a gradient distribution state with gradually increasing values from top to bottom; after being given a short period of mild drought stress, the chlorophyll content accumulated. Compared with the value before stress, it has improved, but no longer presents a gradient distribution state. At the same time, after severe drought stress, the chlorophyll value decreased as a whole, and the lower leaves began to turn yellow, wilt and fall off; when the stress intensity was consistent with the duration, the effect of drought on the chlorophyll value was 895 < SY-1 < 110 < 3804. This research provides an effective tool for in-depth understanding of the mechanisms and physiological responses of plants to environmental stress. It is of great significance for improving agricultural and forestry production and protecting the ecological environment. It also provides decision-making for solving plant drought problems caused by global climate change.