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Current advances in recommender systems have been remarkably successful in optimizing immediate engagement. However, long-term user engagement, a more desirable performance metric, remains difficult to improve. Meanwhile, recent reinforcement learning (RL) algorithms have shown their effectiveness in a variety of long-term goal optimization tasks. For this reason, RL is widely considered as a promising framework for optimizing long-term user engagement in recommendation. Though promising, the application of RL heavily relies on well-designed rewards, but designing rewards related to long-term user engagement is quite difficult. To mitigate the problem, we propose a novel paradigm, recommender systems with human preferences (or Preference-based Recommender systems), which allows RL recommender systems to learn from preferences about users historical behaviors rather than explicitly defined rewards. Such preferences are easily accessible through techniques such as crowdsourcing, as they do not require any expert knowledge. With PrefRec, we can fully exploit the advantages of RL in optimizing long-term goals, while avoiding complex reward engineering. PrefRec uses the preferences to automatically train a reward function in an end-to-end manner. The reward function is then used to generate learning signals to train the recommendation policy. Furthermore, we design an effective optimization method for PrefRec, which uses an additional value function, expectile regression and reward model pre-training to improve the performance. We conduct experiments on a variety of long-term user engagement optimization tasks. The results show that PrefRec significantly outperforms previous state-of-the-art methods in all the tasks.