The purpose of this study is to characterize airflow fluctuation, which occurs by the motion of traveling-type large crane, and to improve airflow environment in the clean stockers. Time-dependent change of airflow distribution and particle concentration were simulated using the multi-block simulation technique, and the factors of particle contamination on the surface of glass substrates in the stocker were studied. Clean stocker has rack zone and vehicle’s running zone. Rack area has FFUs (Fan Filter Units) on sidewall and ceiling, and they provide airflow distribution from rack area toward vehicle’s area. However, the traveling motion of the crane makes strong airflow turbulence, and it sometimes brings the invasion of particles from crane zone to rack zone. Countermeasures to the airflow intrusion were also studied. As the result of the study, speed control of the crane and separation of rack area were very effective to avoid the invasion of particles.