Hollow microspheres as the filler material of syntactic foams have been adopted in extensive practical applications, where the physical parameters and their homogeneity have been proven to be critical factors during the design process, especially for high-specification scenarios. Based on double-emulsion droplet templates, hollow microspheres derived from microfluidics-enabled soft manufacturing have been validated to possess well-controlled morphology and composition with a much narrower size distribution and fewer defects compared to traditional production methods. However, for more stringent requirements, the innate density difference between the core-shell solution of the double-emulsion droplet template shall result in the wall thickness heterogeneity of the hollow microsphere, which will lead to unfavorable mechanical performance deviations. To clarify the specific mechanical response of microfluidics-derived hollow silica microspheres with varying eccentricities, a hybrid method combining experimental nanoindentation and a finite element method (FEM) simulation was proposed. The difference in eccentricity can determine the specific mechanical response of hollow microspheres during nanoindentation, including crack initiation and the evolution process, detailed fracture modes, load-bearing capacity, and energy dissipation capability, which should shed light on the necessity of optimizing the concentricity of double-emulsion droplets to improve the wall thickness homogeneity of hollow microspheres for better mechanical performance.