I was in the middle of something when you had called me on the phone. so, I couldn't pick up your call.
Is this sentence correct?
No. You don't need Past Perfect here. , I was in the middle of something when you called me, so I couldn't pick up the phone.
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No.
You don't need Past Perfect here. You are just talking about a Simple Past event.,
I was in the middle of something when you called me, so I couldn't pick up the phone.
Note also that I've tightened up your wording a bit.
Clive
kumenglishI couldn't pick up your call.
This is a bit wordy. In the UK people just say answer instead.