Clustering of iron oxide nanoparticles is a major concern in synthesizing MRI agents as it reduces the effectiveness of in vivo circulation and accurate MRI signaling. Especially on nano scale, lack of fine control on clustering is inevitable. However, in order to gain the conformational control on nanoparticles, various synthesis reaction parameters can be adjusted to construct the most ideal conformation possible, as well as to produce least amount of yield loss due to aggregations. Using magnetic iron oxide nanoworms as a model, the effects of clustering were observed through a multivariant testing of the synthesis temperature, reaction time, and pH. Under the optimized settings, the production of longer single-chain nanoworms was possible as well as raising the yield of functional nanoworms.