In transformerless three-level photovoltaic inverter systems, the modified LC filter, which directly connects the dc-side neutral point to the common point of filter capacitors, is considered to be an ideal scheme to suppress the troublesome leakage current. However, a new common-mode (CM) resonant current is emerged, which leads to inverter-side current distortion and even system instability. Therefore, a second-order passivity-based controller in time domain featuring with excellent system stability is proposed for the CM resonant current mitigation. First, the reason of CM resonant current generation with the modified LC filter is analysed in detail. Then, the CM current model is derived, which reveals that it is a second-order system. The passivity of this second-order model is strictly proved. Moreover, based on the passive control theory, zero state detectable theory and Lyapunov stability theorem, a second-order passivity-based controller is designed step by step to suppress the CM resonant current, and the system global asymptotic stability is also proved. The proposed controller is based on time domain, which is more intuitive and avoids the error amplification in the conversion from frequency domain to time domain. Finally, the effectiveness and the correctness of theoretical derivation of the passivity-based control method are validated by experiments. Compared with passive damping resistor method, the proposed method not only has better performance, but also avoids the use of real resistor and reduces the cost by using software instead of hardware.