The flower of Polystachya pubescens is non-resupinate, i.e. not twisted around; its lip presented at the top, as it had developed in the bud. The small lip is three-lobed and flat, 7 mm long; its tiny lateral lobes erect, up to 2 mm tall.

The deep yellow flowers open widely, much more so than those of P. ottoniana. Dull maroon lines are visible in picture upon the upper halves of the lateral sepals and the lip, the upper flower parts.

The sepals are oblong; the smaller, yellow, lateral petals below them obovate. Tiny pointed tips are conspicuous on all three sepals, including the yellow one pointing down, right at the bottom of every flower in picture.

Some of the plants have fragrant flowers, but not all. The pollination system of this species is not yet known (Liltved and Johnson, 2012; www.orchidspecies.com).