I have 2002 toyota sienna XLE. I can use key to control the power sliding door opening and closing when the door is not closed. However, when the door is close, I can not use key to control it. I can only hear some noise, but I touch the door handle twice, it will be automic opening,and I still can use key to close to door.

SOURCE: 2005 Toyota Sienna XLE - Automatic sliding door not closing.

This may or may not work depending on exactly what is wrong with the door, I cant tell what is wrong without looking at it directly however:
You can try starting with all doors closed and unlocked, keys in hand disconnecting the battery and letting the vehicle sit for 2 min or so, then reconnect the battery. Put the key into the ignition and turn it to the on position but do not start the van. Next press the button to disable the power sliding door for the drivers side, then manually open the door fully, wait 5 seconds, then close it manually fully. Press button the button again to re-enable the power sliding door, then try to use it with the automatic feature either by pulling the handle or using your remote, this may or may not work depending on if the door has somehow become de-initialized (it should work now) however if something is broken inside the door closing mechanism or door closed/open sensors, the door will continue to malfunction.