The invention relates to a high repetition frequency jamming-resistant laser encoding method. Due to the threat of high repetition frequency laser active jamming to the laser semi-active homing guidance, aiming at a tunable laser generating nanosecond level pulse width, the invention provides the encoding of pulse width and pulse amplitude by directly clipping with an electro-optical switch; the phase difference generated by static double refraction is compensated by an orthorhombic KTP (potassium titanium oxide phosphate) crystal; the delay and the error can be reduced due to the synchronous control of a pockels cell power supply; the laser encoding, the pulse width encoding and the pulse amplitude modulation are combined with one another, so that the PAWM (puto amo window manager) encoding which not only can resist the laser angle deception jamming but also can resist the high repetition frequency jamming can be formed; and the method of high repetition frequency jamming resistance is improved on a guidance head, so that a novel laser encoding system can be formed, wherein the system is suitable for the aspects such as tracking, guidance, positioning, collimation, photo-communication APT (arbitrage pricing theory) technology, and photoelectronic warfare.