The invention belongs to the technical field of plant root system detection, and provides an automatic plant root system monitoring system. Under the premise of not injuring the original plants, the growing states of root systems can directly viewed through organic glass soil columns, a plant root system monitoring subsystem acquires the soil moisture, temperatures and plant evaporation capabilities of a variety of plant root systems and data and images as plant root system growth parameters in real time, dynamically and in all weathers, a plant root system and leaf analysis subsystem carries out analysis on the plant root system images and the leaf images, and investigates the relation between the growth of the leaves and the growth of the root systems, and the moisture, nutrient, temperature and microbial indexes of rhizosphere soil can be monitored and sampled by observing openable small windows on the organic glass soil columns, so that the determination and analysis of various physiological and biochemical indexes and a root-cutting experiment can be carried out. The automatic plant root system monitoring system reduces errors produced by a single large field experiment, provides powerful data sources for more in-depth researches, and has the advantages of little risk, easy maintenance, wide application range and high operability.