At length, he arrived in a place where camel-drivers usually stop to rest their camels. While he was there, waiting anxiously for the arrival of someone of whom he might obtain some food, he spied a little box, almost buried in the sand.
I looked up the dictionary and found the structure "obtain something from someone". But here, the writer use "of". Is it more natural if I change the sentence into "... someone from whom he might obtain some food..."?
Yes. obtain something of someone is old-fashioned English.
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Stylistically this fits the context - camel-drivers resting their camels - very well. "From whom" would be more modern-sounding, but overly grammatical and pedantic.