Abstract The accumulation of catalyst dust at the honeycomb seal for a long time will lead to the honeycomb seal cell blockage, weaken the seal effect of the honeycomb seal, and directly affect the safe and stable operation of the flue gas turbine. Therefore, a research on the influence of honeycomb cell blockage on the seal leakage characteristics is carried out. The flow field model of honeycomb seal is established, and the influence of cell blockage on the leakage characteristics of honeycomb seal is analyzed. A seal leakage characteristic experiment bench is built, and the numerical simulation results are verified by the experiment bench. Compared with the honeycomb seal without blockage, the leakage of the honeycomb seal with a blockage rate of 25% increases by about 6.5%, while the leakage of the honeycomb seal with a blockage rate of 25% obtained by the experiment increases by about 6.3%. The numerical simulation results are in good agreement with the experimental results. The results of this research provide theoretical support for revealing the seal leakage characteristics of honeycomb seals under blockage faults.