Magnetic Janus particles (MJPs) with compositional compartmentalization and strong magnetic responsiveness play a pivotal role in various application fields, such as biotechnology, medicine, and materials science. However, comprehensive reviews of the field of MJPs remain limited. Here, this article attempts to fill the gap by reviewing the current common synthetic strategies for MJPs, including masking, microfluidics, self-assembly, phase separation, and seeded emulsion polymerization, among others. It then covers the multifunctional applications of MJPs, beneficial from their magnetic properties and anisotropic topological structure, primarily involving environmental remediation, biomedicine, smart displays, interfacial catalysis, emulsion stabilization, and structured liquid materials are presented, as well. Finally, the current challenges and future perspectives for MJPs are also discussed, aiming to fully harness the potential for broader applications.