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Abstract One-unit-cell FeSe films on SrTiO3 substrates are of great interest owing to significantly enlarged pairing gaps characterized by two coherence peaks at ±10 meV and ±20 meV. In-situ transport measurement is desired to reveal novel properties. Here, we performed in-situ microscale electrical transport and combined scanning tunneling microscopy measurements on continuous one-unit-cell FeSe films with twin boundaries. We observed two spatially coexisting superconducting phases in domains and on boundaries, characterized by distinct superconducting gaps ( $${\Delta }_{1}$$ Δ 1 ~15 meV vs. $${\Delta }_{2}$$ Δ 2 ~10 meV) and pairing temperatures (T p1~52.0 K vs. T p2~37.3 K), and correspondingly two-step nonlinear $$V \sim {I}^{\alpha }$$ V ~ I α behavior but a concurrent Berezinskii–Kosterlitz–Thouless (BKT)-like transition occurring at $${T}_{{{{{{\rm{BKT}}}}}}}$$ T BKT ~28.7 K. Moreover, the onset transition temperature $${T}_{{{{{{\rm{c}}}}}}}^{{{{{{\rm{onset}}}}}}}$$ T c onset ~54 K and zero-resistivity temperature $${T}_{{{{{{\rm{c}}}}}}}^{{{{{{\rm{zero}}}}}}}$$ T c zero ~31 K are consistent with T p1 and $${T}_{{{{{{\rm{BKT}}}}}}}$$ T BKT , respectively. Our results indicate the broadened superconducting transition in FeSe/SrTiO3 is related to intrinsic electronic inhomogeneity due to distinct two-gap features and phase fluctuations of two-dimensional superconductivity.