The sentence is in passive voice. You can't say "The process which liquid substances are produced ------" This doesn't make any sense. You could, however, use "in" instead of "by", but 'by' is better because it indicates that 'process' is the actor and 'liquid substances' are the result of the action.
Secretion is the process by which liquid substances are produced by parts of the body or plants."Secretion: the process by which liquid substances are produced by parts of the body or plants."
That isn't a sentence; it's a definition. This is a sentence:
"Secretion is the process by which liquid substances are produced by parts of the body or plants."
"A bicycle is the vehicle by which I get to work."
"A bicycle is the vehicle [which] I get to work by."
"I get to work by bicycle."
"This is the philosophy by which I live."
"This is the philosophy [which] I live by."
"I live by this philosophy."
It's clear now. Thanks! I have another question about why use preposition "by" but not " through" - " through which"?Well, "which" refers to "process", but "secretion" is the process. So, yes indirectly, it's the same thing. The same occurs in my first example, in which "which" refers to "vehicle", but "vehicle" refers back to "Bicycle".
Note my use of "in which" in the previous sentence. The principle is same.
PS: You could leave out "the process by which" and say:
"By secretion, liquid substances are produced by parts of the body or plants."
"Liquid substances are produced by parts of the body or plants by secretion."