Long-Term Evolution in unlicensed spectrum (LTE-U) is a promising solution to address the spectrum scarcity in the cellular networks. However, the LTE-U and WiFi systems may interfere with each other and degrade the performance. Thus, many works have focused on coexistence design and proposed various solutions. Nevertheless, the hidden terminal problem has not been well studied in the LTE-U system. In this paper, we investigate joint interference detection and resource allocation in the LTE-U system to maximize the overall system throughput while guaranteeing each user's quality-of-service (QoS) requirements. Firstly, to solve the hidden terminal problem and avoid the co-channel interference between the WiFi and LTE-U users, we adopt a cluster-based algorithm to find the potential WiFi interference for each LTE-U user according to their channel quality indicator (CQI) feedback and location information. Secondly, we formulate a joint subcarrier and power allocation problem over the licensed and unlicensed bands with each user's QoS provision. To make the original problem more tractable, we separate it into licensed and unlicensed subproblems and then derive the optimal solution. Moreover, we propose a low-complexity resource allocation scheme. The simulation results show that the proposed schemes can significantly improve the system performance and outperform the existing schemes.