QUOTE
What is the origin of the phrase?
clean someone's clock
QUOTE
Beat, thrash, or defeat someone decisively, as in "He's much bigger than you and could easily clean your clock". This term originated in the military. The use of clock is unclear but possibly alludes to hitting someone in the face (for "clockface"). [Slang; mid-1900s]
Source: The American Heritage® Dictionary of Idioms by Christine Ammer.
Copyright © 1997 by The Christine Ammer 1992 Trust. Published by Houghton Mifflin Company.
When in doubt, check the dictionary.

Loretta
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I checked The Oxford English dictionary website as well as Websters, they do not know the origin!