'multinucleate' is formed in English from the combining form 'multi-' meaning 'many' (from Latin 'multus') + 'nucleate' (from Latin 'nucleus' meaning 'kernel' or 'core'), i.e. literally 'having many nuclei'.

'nucleate' comes from Latin 'nucleus' (meaning 'kernel, little nut'), which passed into scientific Late Latin/Neo-Latin forms and then into English; 'multinucleate' was coined in scientific English by combining the prefix 'multi-' with 'nucleate' to describe cells with multiple nuclei.

Originally elements 'multi-' and 'nucleate' retained their separate senses ('many' + 'having a nucleus'); over time the combined form came to be used specifically in biology to describe cells or structures that contain multiple nuclei.