Prevailing models of the evolutionary prisoner’s game on networks always assume that agents are pursuing their own profit maximization. But the results from experimental games show that many agents have other-regarding preference. In this paper, we study the emergence of cooperation from the prisoner’s dilemma game on complex networks while some agents exhibit other-regarding preference such as inequality aversion, envious and guilty emotions. Contrary to common ideas, the simulation results show that the existence of inequality aversion agents does not promote cooperation emergence on a BA (Barabási and Albert) scale-free network in most situations. If the defection attraction is big and agents exhibit strong preference for inequality aversion, the frequency of cooperators will be lower than in situations where no inequality aversion agents exist. In some cases, the existence of the inequality agents will even induce the frequency of cooperators to zero, a feature which is not observed in previous research on the prisoner’s dilemma game when the underlying interaction topology is a BA scale-free network. This means that if an agent cares about equality too much, it will be difficult for cooperation to emerge and the frequency of cooperators will be low on BA networks. The research on the effect of envy or guilty emotions on the emergence of cooperation in the prisoner’s dilemma game on BA networks obtains similar results, though some differences exist. However, simulation results on a WS (Watts and Strogatz) small-world network display another scenario. If agents care about the inequality of agents very much, the WS network favors cooperation emergence in the prisoners’ dilemma game when other-regarding agents exist. If the agent weight on other-regarding is lowered, the cooperation frequencies emerging on a WS network are not much different from those in situations without other-regarding agents, although the frequency of cooperators is lower than those of the situation without other-regarding preference agents sometimes. All the simulation results imply that inequality aversion and its variations can have important effects on cooperation emergence in the prisoner’s dilemma game, and different network topologies have different effects on cooperation emergence in the prisoner’s dilemma game played on complex networks.