Rice production could be increased by System of Rice Intensifications, that is water-saving, fertilizer-saving, and production cost-saving. Using quality varieties could increase the production of rice. This research analyzed the physiological growth and yield on varieties of rice plants, with intermittent irrigation on SRI. This research was conducted in the Faculty of Agriculture, Universitas Muhammadiyah Yogyakarta from July to November 2017. This research was arranged in a 5 x 2 factorial design in Completely Randomized Design with three replications. The first factor consisted of five rice varieties i.e. IR-64, Mekongga, Inpari Sidenuk, Ciherang, and HIPA-18. The second factor was irrigation, consisting of two levels, i.e. SRI and conventional methods. The results of this research showed that the Harvest Index of IR-64 was higher than those of Ciherang and HIPA-18. Inpari Sidenuk variety had the lowest Harvest Index. The grain weight and unfilled grain weight of Ciherang, HIPA-18 and Mekongga were better than those of Inpari Sidenuk. SRI irrigation affected the fresh weight and root length of rice plants. SRI irrigation conditions produced heavier fresh weight and longer root than conventional irrigation. SRI irrigation conditions produced heavier fresh weight and longer root than conventional irrigation. Productive tillers of IR 64 variety with irrigation treatment using SRI was higher than Mekongga and Inpari Sidenuk using SRI, and Inpari Sidenuk using conventional irrigation method.