A gas turbine system burning heavy-oil modified fuel and a method of operating the gas turbine system, which covers from a stage of modifying heavy oil and producing gas turbine fuel to a stage of operating a gas turbine, including startup, ordinary shutdown and emergency shutdown of the gas turbine. The gas turbine system burning heavy-oil modified fuel comprises a reactor for mixing heavy oil and water to cause reaction, thereby separating and removing a heavy component from the heavy oil, a gas-liquid separator for separating hydrocarbon gas and modified oil obtained in the reactor from each other, a gas turbine combustor for burning the hydrocarbon gas supplied from the gas-liquid separator, and a gas turbine driven by combustion gas produced in the gas turbine combustor. The system further comprises another line for extracting the hydrocarbon gas externally of a relevant system region. The other line is branched from a line for supplying the hydrocarbon gas from the gas-liquid separator to the gas turbine combustor.