Recent studies indicate that Rice-Wheat System in the Indo-Gangetic Plains is now facing a number of stresses resulting in slowdown in productivity growth. It is now important to study and empirically verify through in depth analysis the observed trend, yield growth, instability, total factor productivity and sustainability of yield. In this context, the present study has been carried out with following specific objectives; (a) to estimate total factor productivity in rice and wheat to calculate sustainability (b) to study the yield trend and instability in rice and wheat in IGP region. To calculate total factor productivity the data on different inputs and output were used. The input index comprises the data on seed, fertilizer, manure, insecticide, human labor, and animal labor. The data on inputs used and outputs were compiled from the reports of cost of cultivation of important crops in India. The Cuddy-Della Valle Index was used to calculate instability. Deceleration in total factor productivity growth was observed in rice for the period 1990 to 2011. Major changes in yield were observed in UP and Punjab. In Punjab, 8 districts had higher productivity ranging from 3 to 4 ton/ha between 2001 and 2010. Bihar had no significant changes during the period but yield increased by 50% from 200 to 300 kg/ha. There exists scope to increase yield in rice in all the districts of Bihar. In case of wheat, major changes in yield across districts were observed in UP and Haryana. In Haryana 6 districts have moved from 3 to 4 ton/ha in 2001 to more than 4 ton/ha in 2010. Fertilizer, rainfall and electricity had significant positive influence on yield in rice and wheat