Compared with traditional environments, the cloud environment exposes online services to additional vulnerabilities and threats of cyber attacks, and the cyber security of cloud platforms is becoming increasingly prominent. A piece of code, known as a Webshell, is usually uploaded to the target servers to achieve multiple attacks. Preventing Webshell attacks has become a hot spot in current research. Moreover, the traditional Webshell detectors are not built for the cloud, making it highly difficult to play a defensive role in the cloud environment. SmartEagleEye, a Webshell detection system based on deep learning that is successfully applied in various scenarios, is proposed in this paper. This system contains two important components: gray-box and neural network analyzers. The gray-box analyzer defines a series of rules and algorithms for extracting static and dynamic behaviors from the code to make the decision jointly. The neural network analyzer transforms suspicious code into Operation Code (OPCODE) sequences, turning the detection task into a classification problem. Comprehensive experiment results show that SmartEagleEye achieves an encouraging high detection rate and an acceptable false-positive rate, which indicate its capability to provide good protection for the cloud environment.