In this paper, after clarifying the key concepts of spatial form genes and GIS, the overall form of rural settlements is analyzed by using spatial gene inheritance technology. The most important spatial genes are identified, and these genes are inherited in the design to preserve the traditional characteristics and cultural charm of the countryside. The effectiveness of the application of the spatial gene inheritance technique is evaluated by using various methods such as field surveys, qualitative research, inductive deduction, and combining with specific rural cases. After the optimization of the ecological landscape, the ecological landscape service value of L countryside increased significantly, including food production increased by 32.90% compared with that before optimization. The sensitivity of the optimized ecological landscape was also calculated to be reduced to 0.074~0.86. In addition, in terms of ecological landscape genetic inheritance, the overall score of the spatial elements of the optimized ecological landscape was the highest in the L countryside. The results of the questionnaire survey showed that the residents were highly satisfied with the effect of this paper’s method on the preservation of traditional features in the ecological landscape of the countryside.