This paper studies a Markovian clearing queuing system with setup times in alternating environment. At the completion of exponential service cycles, the server removes all present customers. The system operates in an alternating environment which may influences the arrival rate of the customers and the transportation facility (i.e., service rate). Upon their arrivals, customers decide whether to join or balk the system based on a natural linear “rewardcost” structure. According to the different states of system, we derive the balking strategies of customers, the stationary distribution of system state, the mean queue length and the social optimal benefit. Finally, some numerical examples are presented.