This article presents a reactive distillation simulation model of biodiesel production from the feed of 1,000 kg/h Jatropha oil. Starting with the verification of the conventional process at the purification sections and improve transesterification calculation, the model gives a realistic solution. GaussViewW and GAUSSIAN 03W are used to generate the molecular structure for other key compositions including triglyceride, diglyceride, and monoglyceride of oleic and linoleic acid which are major components of Jatropha oil. The biodiesel conversion 1.14 % and energy 1.36 %; requirement by the reactive distillation process are higher than the conventional process which the conversion of conventional process and reactive distillation are 98.2 and 99.8 respectively. However, reactive distillation can almost consume the reactant completely. While there are some triolein and diolein in biodiesel from the conventional process, these residues impact on the quality of biodiesel. The recycling system can also reduce fresh methanol by about 81%. The optimum conditions of reactive distillation are 2 stages of the reaction zone, no rectifying section, no stripping section, 5 reflux ratio, and 1 atm. The controllability of the process is studied by varying the feed oil ± 2%. The control structure of the process can handle these disturbances and keep the product at the desired specification.