The present invention relates to an improved reactor, which allows microwave-assisted processing of feedstocks or mixtures of hydrocarbons, and the operating system thereof, which operates under high temperatures and pressures of hydrogen or other gases, in continuous of batch mode. The invention relates to modifications in the geometric configuration of the reactor to process diverse hydrocarbon feedstocks, with or without the addition of catalysts, in the presence or absence of hydrogen or other gases, forming a system which includes a reaction vessel and associated devices, so as to to allow better transmittance of the radiation onto the feedstock to be processed and guarantee maximum absorption of the microwaves by the the reaction medium irrespective of the composition thereof.