Lean premixed prevaporized combustors often feature staged combustion with a premixed main flame anchored by the nonpremixed pilot flame to obtain a wide operating range. Interaction between pilot flame and main flame is complex. The present article investigates the flame topologies and flame-fuel interactions in separated stratified swirl flames under various operating conditions (fuel to air ratio FAR and fuel stage ratio α) and injector designs (main stage swirl number Sm and fuel injection angle JA). Experiments are carried out in the centrally staged optical model combustor at inlet pressure P3 = 0.49–0.7 MPa and inlet temperature T3 = 539 K. At first, the flame structures obtained from OH-PLIF are investigated and discussed for the baseline injector (Sm = 0.9, JA = −50°). The V-shaped flame is stabilized in the inner shear layer (ISL) with the flame attachment point located at the lip for the pilot flame mode (α = 1). Dual flame is observed in the combustor for the fuel staged combustion (α < 1): the main flame stabilized in the outer shear layer (OSL) and the pilot flame stabilized in the inner shear layer (ISL). For increasing α from 0.15 to 0.25, gaps between the main flame and pilot flame are decreased, indicating a stronger interaction between the two flames. The flame structure for different injector geometries is then investigated. It is found that the higher main stage swirl number induces a larger flame opening angle, decreasing the interaction between two flames. Fuel injected into crossflow (JA = −50°) is found to generated a more separated flame, decreasing the flame interactions. Finally, fuel distribution measured by kerosene-PLIF is analyzed with the correlation to flame structure. Results show that the existence of a good mixing of fuel and fresh air in ISL and OSL provide favorable conditions for chemical reaction with high heat release. The OH distribution is highly correlated to fuel distribution. The fuel zone is located at the inner side of high OH region, indicating the reaction and heat release take place after the mixing of preheating of fuel-air mixture.