We present Janus microgels modified using a Pickering emulsion-based approach and demonstrate their self-assembly. Stimuli-responsive microgels composed of cross-linked poly[N-isopropylacrylamide-co-(acrylic acid)] (pNA) were synthesized by means of aqueous free-radical precipitation polymerization. Using pNA microgels as stabilizers, a Pickering emulsion was formed by simple stirring with pNA dispersion and hexadecane. The amino groups were then introduced by means of a carbodiimide coupling reaction using ethylenediamine and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. These microgels were collected by emulsion collapse. Hemispherical distribution of the amino groups in the modified microgels was confirmed using the Au nanoparticle labeling technique. Interestingly, these microgels were aggregated in string structures at pH 4, whereas they were not at pH 6. Such microgel string structures self-assembled from well-structured microgels by simple stimuli-change have potential use as micro-actuators.