One of the problems that exists in substrate culture is salt accumulation in root zone, and adequate management of nutrient solution is the primary method to control it. In order to achieve scientific management of nutrient solution, salt accumulation characteristics in root zone need to be studied. A greenhouse experiment was carried out to determine the influence of two systems (open and closed) on electrical conductivity, ion constitution of root solution, nutrient uptake, yield and fruit quality of tomato and nutrient use efficiency. Results showed that electrical conductivity of root solution was increased with the growth of tomato, the highest electrical conductivity in open and closed systems were 11.9 mS/cm and 17.2 mS/cm, respectively. The salt ions in root zone of the two systems were mainly NO3-, K+, Ca2+, Mg2+,SO42- and H2PO4-. The ion imbalance was found in both the open and closed systems, ratios of K+,Ca2+ and H2PO4- concentrations to total ion concentration were decreased from the initial while the ratios of Mg2+, NO-3 and SO42- were increased. The yield of tomato was decreased with high electrical conductivity in open and closed systems, while the blossom-end rot (BER) of fruit was increased with high electrical conductivity and ion imbalance degree. At the end of the trial, the BER in open and closed systems were 29.7% and 36.6%, respectively. Compared with open system, closed system improved the nutrient use efficiency, the nutrient use efficiencies of N, P, K, Ca, Mg and S were increased by 11.6%, 19.6%, 18.9%, 11.8%, 37.3% and 15.9%, respectively. In conclusion, the salt accumulation and ion imbalance existed in open and closed systems. Increasing the input of K and P while controlling the use of Mg, N and S could help to keep the ion balance of root solution. The closed system was a more promising way to realize environment-friendly, water-saving and fertilizer-saving in substrate culture.