In this study, the Input- Output Structural Decomposition Analysis (I-O SDA) is used to investigate the effects of technological structure changes on changes of total output in Sistan and Baluchestan Province during 2006-2011. The technological structure change is decomposed into two factors: intermediate input structure changes (input substitution) and change in direct backward linkage. The results show that the effect of changes in direct backward linkage is negative in all sectors, but the effect of input substitution in twelve sectors is positive and in other nine sectors is negative. Input substitutions in "Agriculture" and "Transport" sectors have the main positive effect on total output of the region and in ''Food industries'' and ''Restaurants & Hotels'' have the main negative effect on total output. This factor caused 20.89 billion Rials decrease in total output of region. Changes in direct backward linkage caused 8270.89 billion Rials decrease in total output of the region.