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At present, substrate cultivation has been widely used for planting a variety of fruits, vegetables and flowers. Since the invention of nutrient solution used in substrate culture techniques, the decision making irrigation methods mainly adopted three ways in greenhouse, i.e. irrigation scheduling respective by time clock and radiation, and a way based on Penmen equation. But there were some defects above the three ways, the first two ways were not considered the demand for water of crops in different time in a day and growth period, leading to the supply more or less, and there were too many parameters to be determined in the last way. The negative pressure irrigation system could supply water for the plants timely and accurately according to the consumption by the plants themselves at any time of a day and the influence of different external environment, which only involved a parameter—consumption, and was easy to operate. An automatic decision making method and system of irrigating nutrient solution in substrate culture in greenhouse based on negative pressure, which allowed us to decide the supply amount for most crops based on a small amount of crops consumption. This automated decision-making system ensured the plant roots in the balanced condition of water and nutrient (EC and pH value), which achieved a more efficient nutrient solution management in the substrate culture. This automated decision-making system adopted the consumed amount of nutrient solution in a line of plants in a certain time, in which line the negative pressure irrigation system was installed. The value obtained from consumed amount of plants of a line multiplying by a leaching-coefficient was used as supply volume for the other plants in substrate culture by drip irrigation system in the next time. The coefficient is related to the amount of drained nutrient solution. Commonly, 25%~30% of the applied nutrient solution should to be drained, which could prevent salt accumulation in the substrate. Moreover, the time and frequency for supply in other lines in one day was determined by the consumed amount of nutrient solution in a line. The consumed amount in a line was measured by flow sensor which was connected with the singlechip in a fixed time, then an order was given by the singlechip to control the work of the magnetic valve and collect the values from flow sensors in the other lines. At the same time, tomato plants in the substrate culture lines were irrigated nutrient solution by time clock as control test. Experimental results showed that the yield per plant of tomatoes that the automatic decision-making system based on negative pressure increased by 6.70% compared with the irrigation scheduling by time clock, while the consumption of nutrient solution decreased by 28.13%. It proved that the automatic decision-making system ran well and was able to supply the tomato plants nutrient solution timely and accurately according to the water requirement regularity of tomato plants per day.