To realize quick design of the gyro-klystron amplifiers, a kind of numerical simulation method based on the single mode self-consistent nonlinear theory of gyrotrons was investigated. The single mode theory can’t be used to match the disrupt boundary conditions of the input and the middle cavities of the gyro-klystrons, thus the input and the middle cavities can only be processed through single mode theory based on given field distributions. As for the output cavities with smooth boundaries at the power output ends, the single mode nonlinear simulation could be self-consistent. A millimeter wave two cavity gyro-klystron amplifier with reported detailed parameters was simulated using the developed single mode theory. The effectiveness of the numerical simulation was verified by comparing the simulation results with those obtained in a commercial particle in cell (PIC) simulation tool.