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Nanoscale structural modulation with different layer numbers in layer-structured complex oxides of the binary Bi 4 Ti 3 O 12 -BiFeO 3 system can give rise to intriguing phenomena and extraordinary properties, originating from the correlated interfaces of two different phases with different strain states. In this work, we studied the nanoscale structural modulation induced by Co-substitution in the Aurivillius-type oxide of Bi 11 Fe 3 Ti 6 O 33 with a unique and naturally occurred mixed-layer structure. Nanoscale structural evolution via doping occurred from the phase-modulated structure composed of 4- and 5-layer phases to a homogeneous 4-layer structure was clearly observed utilizing x-ray diffraction and electron micro-techniques. Significantly, magnetic response for the samples under various temperatures was recorded and larger magnetic coercive fields (e.g. H c  ∼ 10 kOe at 50 K) were found in the phase-modulated samples. Analyses of the x-ray absorption spectra and magnetic response confirmed that the low-temperature magnetic behaviour should be intrinsic to the phase-modulated structure inside the structural transformation region, mainly arising from structural distortions at the correlated interfaces.