Taking the advantage of the emergy approach in estimating the stability of greenhouse systems leads to the use of correct management methods to increase the stability of production in these systems. In this research, two production systems of cucumber and tomato in Sistan region were assessed, using emergy indices. For this purpose, 166 cucumber and 111 tomato greenhouses were selected. The result of measuring 13 indicators showed the relative stability of the cucumber production system to the tomato system. The highest and lowest values of transformity index in tomato and cucumber systems were 2.77×103 and 2.00×103 (solar MJ per gram), respectively. Physiological characteristics of cucumber such as longer growth period and the greater use of free renewable energies, more production and the effective use of labor, made this system more sustainable, compared to the tomato one. In the tomato production system, the high proportion of purchased non-renewable resources was responsible for unsustainability. In order to increase the sustainability in greenhouse production systems, it is necessary to select plants with a higher capacity in using free environmental energies, capability of a more efficient labor use, and to use of greenhouse structures with the technologies aimed at reducing the inputs and the purchased non-renewable inputs.