Microfluidic study is performed to investigate how multi-walled carbon nanotube (CNTs) aggregates disperse in blend system during morphology evolution. As the dispersed phase, a drop containing CNT is generated at the flow focusing and it deforms through a contraction channel (gap and width of contraction ${sim}100{mu}m$). When an aqueous polymeric drop (2 wt% alginic acid) with CNT (0.05 wt% or 0.5 wt%) is stretched through a 4:1 contraction channel, CNT aggregates enhances breakup of the stretched drop. Also, small droplets including CNTs are pinched off during relaxation of the stretched drop. Based on these observations, it is found that CNTs disperse in a multiphase system by repetitive breakup process during mixing rather than migration driven by chemical affinity.