We developed the intensive multiple sequential batch simultaneous saccharification and cultivation of the selected thermotolerant yeast strain for single-step ethanol production. The selection and high-cell-density inoculum production of thermotolerant yeast able to produce ethanol under the optimal conditions for single-step ethanol fermentation has become a necessity. In this study, the newly isolated Kluyveromyces marxianus SS106 could tolerate high temperatures (35−45 °C) and grow under a wide range of pH values (3.0−5.5), which are the optimum conditions of raw cassava starch hydrolyzing enzyme used in single-step ethanol fermentation. The high-cell-density concentration of K. marxianus SS106 was produced by a single batch and an intensive multiple sequential batch process in a 5-L stirred tank bioreactor using the simultaneous saccharification and cultivation (SSC) method. The single SSC process yielded the yeast cell biomass at a concentration of 39.30 g/L with a productivity of 3.28 g/L/h and a specific growth rate of 0.49 h−1. However, the yeast cell density concentration was higher in the intensive multiple sequential batch SSC than in the single batch process. This process yielded yeast cell biomass at concentrations of 36.09−45.82 g/L with productivities of 3.01−3.82 g/L/h and specific growth rates of 0.29−0.44 h−1 in the first six batch cycle. The results suggested that the intensive multiple sequential batch simultaneous saccharification and cultivation of K. marxianus SS106 would be a promising process for high-cell-density yeast production for use as the inoculum in single-step ethanol fermentation. Furthermore, we also experimented with single-step ethanol production from raw cassava starch by K. marxianus SS106 in a 5-L stirred tank fermenter. This produced ethanol at a concentration of 61.72 g/L with a productivity of 0.86 g/L/h.