As adjectives the difference between inscrutable and complex
is that
inscrutable is difficult or impossible to comprehend, fathom or interpret while
complex is made up of multiple parts; composite; not simple.
As nouns the difference between inscrutable and complex
is that
inscrutable is one who or that which is inscrutable; a person, etc that cannot be comprehended while
complex is a problem.
As a verb complex is
(chemistry|intransitive) to form a complex with another substance.