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In this paper, the effect of Magneto Hydro-Dynamics (MHD) on a polymer chain in the micro channel is studied by employing the Dissipative Particle Dynamics simulation (DPD) method. First, in a simple symmetric micro-channel, the results are evaluated and validated for different values of Hartmann (<i>Ha</i>) Number. The difference between the simulation and analytical solution is below 10%. Then, two types of polymer chain including short and long polymer chain are examined in the channel and the effective parameters such as <i>Ha</i> number, the harmony bond coefficient or spring constant (<i>K</i>), and the length of the polymer chain (<i>N</i>) are studied in the MHD flow. It is shown that by increasing harmony bond constant to 10 times with <i>Ha</i> = 20, the reduction of about 80% in radius of gyration squared, and half in polymer length compared to <i>Ha</i> = 1 would occur for both test cases. For short and long length of polymer, proper transfer of a polymer chain through MHD particles flow is observed with less perturbations (80%) and faster polymer transfer in the symmetric micro-channel.