Improving the resource use efficiency in agroecosystems will increases agricultural productions, while reduces environmental pollutions. In order to evaluate the nitrogen efficiency and balance indicators, a research was conducted in wheat and saffron production systems at Qaenat region (South Khorasan province, Iran) during growing season of 2011-2012. The Indicators were calculated using the method of Organisation for Economic Co-operation and Development (OECD). For this purpose, the necessary information about seed and corms planting rates, fertilizers, crops yields and the area under wheat and saffron were collected by questionnaire and the required coefficients were obtained from various literatures. Results showed that the nitrogen efficiency and balance indicators were significantly different between districts of the studying area for both crops. The highest nitrogen efficiency was related to wheat in Nimbolouk (88.63%) and for saffron was recorded in Sede (18.03%). Also, nitrogen efficiency and balance indicators showed a significant difference between these crops, so that wheat had higher nitrogen efficiency than saffron, which was mainly due to the amount of manure applied in these crops. There was no significant difference between the different ages of saffron farms for nitrogen efficiency and balance. Also, the results showed that there was a significant negative correlation between nitrogen efficiency and balance indicators.