Control of fluid dynamics at the micrometer scale is essential to emulsion science and materials design, which is ubiquitous in everyday life and is frequently encountered in industrial applications. Most studies on multiphase flow focus on oil-water systems with substantial interfacial tension. Advances in microfluidics have enabled the study of multiphase flow with more complex dynamics. Here, we show that the evolution of the interface in a jet surrounded by a co-flowing continuous phase with an ultra-low interfacial tension presents new opportunities to the control of flow morphologies. The introduction of a harmonic perturbation to the dispersed phase leads to the formation of interfaces with unique shapes. The periodic structures can be tuned by controlling the fluid flow rates and the input perturbation; this demonstrates the importance of the inertial effects in flow control at ultra-low interfacial tension. Our work provides new insights into microfluidic flows at ultra-low interfacial tension and their potential applications.