The Rambam outlines his methodology at the beginning of the MT. He clearly says that he will pasken based on midrashie halakha or even the occasional Yerushalmi.
His claim that women cannot serve in positions of serarah, for instance, is based on a Sifre (Devarim), albeit most likely a corrupt manuscript.
Likewise, the Rambam paskens that we lay tefillin on Hol haMoed, since the Yerushalmi says so explicitly, whereas the Bavli is ambivalent (the Kesef Mishne, IIRC, argues that because the Bavli says we don’t write safut on Hol haMoed, this should mean we also don’t lay tefillin then).