It depends on why he is nodding his head. 'In consent' is OK, as is 'in assent', but they have different meanings. What do you intend?
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AnonymousHe nodded his head in agreement. I thought I could replace agreement with consent: his head nodded in consent.I thought so too, so I looked up assent and consent. (www.m-w.com) I don't know if this helps or makes things worse!