Ionic current rectification (ICR) phenomena conventionally occurs in nanopores which dimensions are comparable to the thickness of their electrical double layers. However, the microscale ICR in a micropore can also exist under some conditions. Here, the charged hydrogel filled conical micropore was constructed to realize microscale ICR. To better understand the micropore ICR, the influences of space charge density of the hydrogel, micropore geometry, the hydrogel filling length as well as the electrolyte concentration and pH were investigated. Furthermore, we developed a PEGDA-based hydrogel filled micropore sensing platform which sensing performance was enhanced due to the weakly charged PEGDA. The promyelocytic leukemia (PML)/retinoic acid receptor alpha (RARA) fusion genes and adenosine triphosphate (ATP) were respectively used as model analytes and the measured detection limits of 0.1 pM were achieved. The successful realization of microscale ICR in a homogenous and functional hydrogel filled micropore suggests that the fabrication, characterization and operation of ICR based devices can be more robust and facilitated for the wider applications.