A system for controlling NOx emissions and combustion pulsation levels of a gas turbine having a gas turbine combustion system, having a single combustion chamber and multiple burners, includes a cascade structure having a first and second control level (1, 2), the first level (1) having a device to control NOx emissions and generate combustion pulsation target levels based on the difference between measured and target NOx emission levels, and the second level (2) having a device to control pulsation levels and generate a ratio (γ) of fuel flow to different types of burners or to different stages of each burner. The fuel flow ratio (γ) is based on the difference between the measured and generated target pulsation levels. The control system enables the operation of a gas turbine to meet NOx emission requirements, while maintaining combustion pulsation levels within limits that ensure improved lifetime of the combustion system.