In this study, for the first time, l-cysteine acted as both the reducing agent and soft template to control the synthesis of selenium nanospheres and nanorods by a novel and mild solution method. The effect of different reactant concentration ratios, reaction times, and ultrasonication on morphologies and crystalline phases of the products was investigated. As-prepared products were characterized by transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM) images, selected area electron diffraction (SAED), X-ray diffraction (XRD) patterns, UV−vis, Raman spectroscopy, and thermogravimetric analysis/differential scanning calorimetry (TGA/DSC) curves, etc. The results showed that the red spherical amorphic nanoselenium was slowly obtained at room temperature. By varying the concentration ratio of l-cysteine to selenious acid, the morphologies and crystalline phases of nanoselenium were not changed, but the diameter of nanoselenium was different. By means of high intensity ultrasonication, gray rodlike t-Se was produced. The experiment of dynamic growth of Se nanorods displayed that the spherical amorphous Se was formed first, and then it was quickly changed into gray rod-shaped t-Se by controlling the ultrasonic time. Finally, a model of “sphere breaking−oriented aggregation−growth” is suggested to explain the possible formation mechanism of selenium nanorods in this study.