Sleep: Use sleep powder or sing to put the Zapdos to sleep. This will make Zapdos easier to catch as well as prevent it from attacking.
Ultra Balls: Use Ultra Balls to increase your chances of catching a Zapdos. Use a combination of techniques described above with the ultra ball to capture Zapdos.
Patience and Persistence: Be patient and persistent when trying to catch Zapdos. It may take some time and multiple attempts, but eventually, you should be able to capture it.