In order to understand the effect of microstructure on the magnetic properties of thin films, we are reporting Fe thin film of two different thicknesses prepared via electron beam deposition on Si (100) substrate whose structural and magnetic properties have been studied using different characterization techniques. The structural measurements carried out using XRD and XRR techniques show variation in structural properties with change in film thickness. The magnetization measurements show increase in coercivity and change in loop shape when the film thickness was changed from 5 nm to 40 nm. The overall results are correlated in terms of thickness induced changes in structural properties which in turn influence the magnetic properties of the film.