In arid and semi-arid regions due to restriction of access to fresh water resources for agricultural production, the major source of irrigation water is salt water. It was argued that the use of magnetic technology and salt water pass through a magnetic field can be helped to improve crop yield where salt water is used. In this regard to investigate effect of salt water passes through the magnetic field on the growth characteristics and yield components of green pepper, an experiment was conducted as completely randomized with split plot design by six treatments and three replications at University of Shahrekord in the summer of 2013. Treatments included two water levels (magnetic and non-magnetic) and salinity at three levels (0.3, 2.3 and 4.2 dS/m). The results showed that magnetic water increases of 12, 19 and 33 percent of the total fruit yield in irrigation water with salinity respectively 0.3, 2.3 and 4.2 dS/m. Also all yield components of the including fresh and dry weight of leaves, stems, roots and root volume of treated water with salinity of 0.3 dS/m highest values than the two others. Magnetic water increases 15 and 11 percent in the weight of stems in salinity of 2.3 and 4.2 dS/m than other non-magnetic levels of its.