Selective Area Metal-Organic Chemical Vapor Deposition (SA-MOCVD) is a promising technique for the scale-up of nanowire fabrication. Our previous study investigated the growth mechanism of SA-MOCVD processes by quantifying contributions from various diffusion sources. However, the edge effect on nanostructure uniformity captured by skirt area diffusion was not quantitatively analyzed. This work further improves our understanding of the process by considering the edge effect as a superposition of skirt area diffusion and “blocking effect” and optimizing the edge effect for uniformity control of nanowire growth. We directly model the blocking effect of nanowires in the process of precursor diffusion from the skirt area to the center of a substrate. The improved model closely captures the distribution of the nanowire length across the substrate. Physical interpretation of the edge effect is provided. With the established model, we provide a method to optimize the width of the skirt area to improve the predicted structural uniformity of SA-MOCVD growth.