Linear codes and $t$-designs are interactive with each other. It is well known that some $t$-designs have been constructed by using certain linear codes in recent years. However, only a small number of infinite families of the extended codes of linear codes holding an infinite family of $t$-designs with $t\geq 3$ are reported in the literature. In this paper, we study the extended codes of the augmented codes of a class of binary cyclic codes with three zeros and their dual codes, and show that those codes hold $3$-designs. Furthermore, we obtain some shortened codes from the studied cyclic codes and explicitly determine their parameters. Some of those shortened codes are optimal or almost optimal.