Men generally only acknowledge something by nodding their heads if they agree with what is being said.
Women nod their heads to indicate that they are listening, not that they agree with what is being said.
Bridge the Gap
Men use as many as 13,000 fewer words in any given day than women. This means that gestures, such as the nodding of a head are more significant to a man. A nod that only indicates listening would seem like a waste of time to a man – his nod needs to mean something – and to him, it means he agrees with you.
Women, being more verbal, place less significance on gestures and more significance on words. A nod, therefore is less important – it just means yup, I heard you.
In this instance, there isn’t really anything you need to change, except your understanding of what your guy means when he nods his head – and what his interpretation of you nodding your head will be. You nod – he sees “Yes, she agrees with me.” To you, you nod and mean “Yes, I hear you talking.”
The misinterpretation of a head nod means you are not getting the right message, and it could be all downhill from there. Since he is nodding to tell you he agrees, but when you nod, you are nodding to acknowledge that a conversation is either taking place or about to take place, it seems easy to see how a wrong message can be sent and received.