This study numerically investigates the effects of a moving crane and airflow on contaminant removal efficiency of various reticle box coverage sequences in a stocker. The analyzed characteristics of flow patterns are used to protect the reticles from contaminants, without altering their internal component configuration in conjunction with the aim of cost-savings. A finite volume method was applied in a numerical analysis using computational fluid dynamics software, ANSYS Fluent. To simulate actual operating conditions, the effects of inlet velocity of clean air and crane movement speed on contaminant removal efficiency (CRE) are considered, and a particle release technique is analyzed to determine contaminant concentrations in the stocker. The results show that a higher airflow rate leads to a better contaminant removal efficiency in the stocker. For the various arrangements of reticle boxes in the stocker, the symmetric coverage sequence provides the most satisfactory contaminant removal rate. An optimal inlet airflow velocity of 0.12 m/s is obtained based on the CRE distribution. In addition, the airflow distributions indicate that a vortex is induced by the air flow through a solid boundary; thus, a higher inlet airflow velocity results in a small vortex that also benefits the CRE. The results also demonstrate that a high crane movement speed causes a large reverse flow region at the bottom that also induces a long wake behind the crane, into which particles are easily drawn.