Laser pulse encoding of laser semi-active guided weapon is an important measure to resist the laser decoy jamming. To a certain extent, existing laser pulse encoding methods have regularity, are identified and cracked by jamming system easily, making laser semi-active guided weapons threatened. A time-controlled laser pulse interval encoding method was proposed. First the encoder was timed by BeiDou module to get absolutely precise time, taking the precision moment (hour, minute, second) as parameters, according to the encoding base frequency, time intervals of the pulses required were generated at the current precision moment by the encoding function only once. Then in the subsequent precision moment, pulse signals with pulse width adjusted were generated at time interval using the timer. Finally, the effectiveness and superiority of the method were verified by numerical simulation and real experiments. Experimental results indicate that timing accuracy is 20 ns, and pulse encoding accuracy is less than 30 ns. The method is characterized by various time intervals of pulses, without any regularity and period, small calculating amount of the encoding function, easy to implement, and strong anti-decoding capability.