Anisotropic microparticles have plenty of applications for their asymmetric structure and precisely modified surface. In our research, the uniform anisotropic microparticles with benzyl chloride group were synthesized successfully via emulsion interfacial polymerization. By varying the degree of cross-linking and the concentration of slightly hydrophilic monomer 4-vinyl benzyl chloride (VBC), several types of microparticles with different concavities and different shapes of microparticles (hemisphere, bowl-like, egg-like, etc.) were obtained. Nanoporous microparticles with a walnut-like heterostructure were achieved with modified hydrophilic seeds with the same strategy. The potential applications of shape-controllable fluorescent microparticles and surface modification of microparticles by thiol-click reaction were explored. The modified microparticles achieved in this study are very useful in labeling, tracing, protein separation, and other biomedical fields.