The cobalt control rods of High Flux Engineering Test Reactor (HFETR) have been in service for over 20 years. In this paper, the burnup of 59Co in HFETR and its effect on the worth of cobalt control rods are calculated and analyzed. The results show that the average burnup and maximum burnup of 9#~14# shim-rod is 4.02% and 5.45%, respectively, and that of 4# and 7# shim-rod is 6.45% and 10.38%, respectively. Considering the effect of 59Co burnup, the worth of 9#~14# shim-rod is almost unchanged, and the worth of 4# and 7# shim-rod decreases 0.15 βeff (for HFETR, 1βeff=0.0071). The sub-criticality decreases 0.16βeff because of 59Co burnup, but the position of the shut-down rod is almost unchanged. So, the effect of 59Co burnup is small, with no effect for the safety of HFETR operation.