As multilayer networks are widely applied in modern society, numerous studies have shown the impact of a multilayer network structure and the network nature on the proportion of cooperators in the network. In this paper, we use Barabási–Albert scale-free networks (BA) and Watts and Strogatz networks (WS) to build a multilayer network structure, and we propose a new strategy-updating rule called “cooperation-defection dominance”, which can be likened to dominant and recessive traits in biogenetics. With the newly constructed multilayer network structure and the strategy-updating rules, based on the simulation results, we find that in the BA-BA network, the cooperation dominance strategy can make the networks with different rs show a cooperative trend, while the defection dominance strategy only has an obvious effect on the network cooperation with a larger r. When the BA network is connected to the WS network, we find that the effect of strategy on the proportion of cooperators in the network decreases, and the main influencing factor is the structure of the network. In the three-layer network, the cooperation dominance strategy has a greater impact on the BA network, and the proportion of the cooperators is enhanced more than under the natural evolution strategy, but the promotion effect is still smaller than that of the two-layer BA network because of the WS network. Under the defection dominance strategy, the WS layer appears different from the first two strategies, and we conclude through simulation that when the payoff parameter is at the middle level, its cooperator proportion will be suppressed, and we deduce that the proportion of cooperators and defectors, as well as the payoff, play an important role.