Five-level active neutral point clamped (5L-ANPC) inverter topologies have gained attention due to their reduced voltage stress and lower dv/dt. This paper investigates a typical single-phase cascaded 5L-ANPC topology with a flying capacitor (5L-ANPC-FC). Considering phase-shift modulation and active flying capacitor voltage (FCV) balancing, the neutral point voltage (NPV) fluctuation is analyzed using an equivalent circuit model that accounts for the limitations of DC-link capacitors. Analysis shows that NPV fluctuation introduces harmonic distortion in the AC current and degrades control performance. To address this issue, a improved modulation strategy is proposed to suppress harmonic distortion. Additionally, a model-based observer is developed to estimate instantaneous NPV without sensors. The proposed circuit model and observer are validated through MATLAB/Simulink simulations. Experimental results tested with a 34kW prototype further confirm the effectiveness of the NPV estimation and modulation strategy in improving output performance.