Compared with the conventional central Shunt Active Power Filter (SAPF), modular designed SAPF can track the harmonics more precisely and quickly with a compact and expandable structure, which makes it a better solution for harmonic mitigation. But there are very few paper discussed about the modeling and parallel resonance issues of modular SAPF parallel system. This paper provides a modeling of three level SAPF, aiming to guide the modular design and research the parallel resonance control method. Firstly, a simplified modular three level SAPF modeling is proposed based on averaging impedance modeling and small signal linearization techniques. Then the coupling issues between modules are researched, and a self-adaptive active damping method is proposed to suppress the system resonance. Based on the modeling results, an improved three level SAPF module topology is proposed to construct the modular system. The theoretical analysis and experimental results verify that the module topology improvement together with the damping strategy can promise the compensating bandwidth, reliability and fast, precise harmonics tracking ability.