In modeling of job shop multi-line facility layout problem, the properties of product also impact the logistics cost. To avoid neglecting of these impactions, in this paper, logistics is replaced by the Equivalent Logistics. On the basis of limitation analysis of quadratic assignment problem, an improved genetic algorithm is proposed. And the encoding, reproduction and fitness functions of are well designed of all 3 layouts. At last, a concrete case is carried out to evaluate the pros and cons of three layout strategies. The layout using automatic new row strategy is proved to be the optimal solution. The result shows that the algorithm can provide reference to related study.