The facts associated with the efficiency of Q- switched Yb∶YAG are overviewed. The rate equation of laser diode end pumped Yb∶YAG is given. The net pumping quantum yield under two-pass end-pumped condition is deduced. With the numerical method,the relationship between the net pumping quantum yield and the length of crystal,the duration of pumping are simulated,and it is concluded that the optimization of the length of crystal is very important for improving the output efficiency of Yb∶YAG laser. The maximum gain, maximum stored energy are also calculated, and the influence on stored energy by amplified spontaneous emission is considered. The optimized design method for Q-switched laser diode end pumped rod Yb:YAG laser is proposed. The analysis and simulation result is helpful for the development of a practical laser system.