We discovered a fractional Chern structure in chiral superconducting Sr$_2$RuO$_4$ nanofilms by employing electric transport. By using Sr$_2$RuO$_4$ single crystals with nanoscale thickness, a fractional Hall conductance was observed without an external magnetic field. The Sr$_2$RuO$_4$ nanofilms enhanced the superconducting transition temperature to about 3 K. We found an anomalous induced voltage with temperature and thickness dependence, and the switching behavior of the induced voltage appeared when we applied a magnetic field. We suggest that there was fractional magnetic-field-induced electric polarization in the interlayer. These anomalous results are related to topological invariance. The fractional axion angle $theta=pi/6$ is determined by observing the topological magneto-electric effect in Sr$_2$RuO$_4$ nanofilms.
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