Determination of trace elements in cells is critical to metallomics research and still faces tremendous difficulties even with the help of highly sensitive inductively coupled plasma mass spectrometry (ICP-MS). Microfluidic chips offer a functional tool-set for cell analysis with features of miniaturization, integration and automation. In this work, we proposed a chip-based array magnetic solid phase microextraction (MSPME) system and on-line combined it with ICP-MS via microflow concentric nebulization for the determination of trace Cu, Zn, Cd, Hg, Pb and Bi in cells. Under the optimized conditions, the limits of detection of the developed on-line chip-based array MSPME-ICP-MS system are 49, 43, 4.2, 6.1, 13 and 18 ng L⁻¹ for Cu, Zn, Cd, Hg, Pb and Bi, respectively. The proposed method was applied to the analysis of target heavy metals in three kinds of cells (HepG2, Jurkat T and MCF7), and the recoveries for the spiked samples were in the range of 83.8%–117%. The extractable species of the target metals in cells were also studied and the results demonstrated a high selectivity of the developed methods towards free metal ions and/or their small molecular species.