Calcium alginate (Ca-alginate) hydrogel microspheres, distinguished by their unique viscoelastic attributes, have found valuable utility in encapsulating bioactive components and facilitating targeted release applications. However, the rapid profiling of the viscoelasticity of these hydrogel microspheres has posed a significant challenge. In this study, we have developed a continuous-flow methodology for swift viscoelastic profiling of a substantial population of hydrogel microspheres, employing embedded electrode pairs and validated with 0.5–2.0% w/v Ca-alginate hydrogel microspheres. Our approach involves the measurement of microsphere size and travel trajectories through the observation of electric signal variations across the embedded electrode pairs. These signals arise from the displacements of the leading and trailing edges of the microspheres. By applying a quasi-linear viscoelastic (QLV) model to interpret the electric signals, we can effectively deduce the viscoelastic properties of the microspheres. Notably, this innovative technique enables fast viscoelasticity screening with a concise constriction channel featuring a minimal number of electrode pairs. The measurement is independent of the applied flow rate. The outcome of our work has led to significantly improved measurement throughput of up to 2650 counts/min for Ca-alginate hydrogel microspheres with 0.5% w/v. Furthermore, this approach can distinguish hydrogel microspheres of varying qualities and chemical compositions based on their viscoelastic properties. This breakthrough holds significant promise for real-time sorting and separation of microspheres, which is particularly useful for developing innovative food structures and texturizers, along with possibilities across a wide spectrum of engineered foods, such as plant-based, printable or bioinspired hydrogels.