With the vigorous development of Internet technology, applications are increasingly migrating to the cloud. Cloud, a distributed network environment, has been widely extended to many fields such as digital finance, supply chain management, and biomedicine. In order to meet the needs of the rapid development of the modern biomedical industry, the biological cloud platform is an inevitable choice for the integration and analysis of medical information. It improves the work efficiency of the biological information system and also realizes reliable and credible intelligent processing of biological resources. Cloud services in bioinformatics are mainly for the processing of biological data, such as the analysis and processing of genes, the testing and detection of human tissues and organs, and the storage and transportation of vaccines. Biomedical companies form a data chain on the cloud, and they provide services and transfer data to each other to create composite services. Therefore, our motivation is to improve process efficiency of biological cloud services. Users’ business requirements have become complicated and diversified, which puts forward higher requirements for service scheduling strategies in cloud computing platforms. In addition, deep reinforcement learning shows strong perception and continuous decision-making capabilities in automatic control problems, which provides a new idea and method for solving the service scheduling and resource allocation problems in the cloud computing field. Therefore, this paper designs a composite service scheduling model under the containers instance mode which hybrids reservation and on-demand. The containers in the cluster are divided into two instance modes: reservation and on-demand. A composite service is described as a three-level structure: a composite service consists of multiple services, and a service consists of multiple service instances, where the service instance is the minimum scheduling unit. In addition, an improved Deep Q-Network (DQN) algorithm is proposed and applied to the scheduling algorithm of composite services. The experimental results show that applying our improved DQN algorithm to the composite services scheduling problem in the container cloud environment can effectively reduce the completion time of the composite services. Meanwhile, the method improves Quality of Service (QoS) and resource utilization in the container cloud environment.