This paper presents a novel approach for automatic, rapid and efficient micro-droplet mixing on ‘open-surface’ droplet-based microfluidics system via magnetic actuation. A two-step micro-fabrication process was employed to decorate the magnetically functionalized polydimethylsiloxane (PDMS) membrane with micro-pillar arrays (MPA) to reduce the adhesion on resident droplets. Droplet manipulation relies on the localized deformation of the elastic membrane under external magnetic fields, thus relieving the additives of magnetic components to the droplets that is commonly required in conventional magnetism-based actuation. Via integration with peripheral computer-based regulator, swift droplet mixing is realized via controlling the coalescent droplets back and forth to generate internal fluid circulations for enhanced mass transfer within the droplet. The comparison of mixing performance between the coalesce-and-stop and back-and-forth mode was systematically performed, which verifies that the back-and-forth actuation of the droplets can obviously improve the mixing efficiency, and typically a higher driving frequency on the droplet renders a shorter mixing duration. With driving frequency of 2.5 cycles/s, the mixing homogeneity can reach 80% within 0.6 s and reach 90% within 1.5 s. Also, it has been experimentally demonstrated that the proposed system can accelerate the dilution under various volume ratios, including 1:2, 1:5, and 1:10. Finally, we demonstrated that the platform can be used to dynamically manipulate the droplets, allowing the de-pinning effect for molecular concentrating and obvious detection sensitivity enhancement in terms of Surface-Enhanced Raman Scattering (SERS). Owing to the superiorities including programmable efficient mixing and parallel scalability, the study herein offers insights for exploiting cost-effective and versatile microfluidics platform for future application in biological analysis, chemical micro-reactions, and trace molecule detections.