Water deficit tension is considered as an important factor in reducing crop yield also, sulfur oxidizing bacteria causes increasing the tolerance of plants to environmental tensions, particularly in maize. In order to investigate the effect of bio-fertilizer Thiobacillus and sulfur on the yield and some biochemical characteristics in grain corn (Zea mays L. Var Maxima) under cut irrigation, a research was conducted with complete randomized blocks design with spilt- plot arrangement in three replications, at research station number two, Islamic Azad University of Varamin in 2014 cropping year. In this experiment, the treatments consisted of water deficit with three levels as the main plot: (control (normal irrigation), cut irrigation in flowering stage and cut irrigation in grain filling stage) and bio-fertilizer Thiobacillus and sulfur in four levels as subplot consisted of control (non-consuming), Thiobacillus bio fertilizer consumption as mixing with seeds when planting, sulfur consumption and combined consumption of Thiobacillus and sulfur. Based on the soil testingthe recommended amount wassulfur fertilizer consumption 250 kilogram per hectare and bio fertilizer Thiobacillus consumption 5 kilogram per hectare. The results of analysis of variance table showed that all of the investigating traits except for the biomarker dehydroxylguanosine were under the effect of water deficit and Thiobacillus. Cut irrigation reduced grain yield, although sulfur and Thiobacillus consumption reduced the negative effect of cut irrigation, the minimum grain yield (4.892 ton per hectare) was achieved at the cut irrigation treatment interaction at flowering stage and non-consumption of Thiobacillus and sulfur so that compared to normal irrigation treatment and combined consuming of Thiobacillus bio fertilizer and sulfur reduced 58.2 percentage. Application of Thiobacillus and sulfur under irrigation cut conditions during critical stages of growth reduced the negative effects of water deficit on grain yield (50 percentage).