Pinus jeffreyi is a large coniferous evergreen tree, reaching 25 to 40 m (82 to 131 ft) tall, rarely up to 53 m (174 ft) tall, though smaller when growing at or near tree line. The leaves are needle-like, in bundles of three, stout, glaucous gray-green, 12 to 23 cm (4.7 to 9.1 in) long. The cones are 12 to 24 cm (4.7 to 9.4 in) long, dark purple when immature, ripening pale brown, with thinly woody scales bearing a short, sharp inward-pointing barb. The seeds are 10 to 12 mm (0.39 to 0.47 in) long, with a large (15 to 25 mm (0.59 to 0.98 in)) wing.
Pinus jeffreyi is closely related to Pinus ponderosa (ponderosa pine) and is similar in appearance. One way to distinguish between them is by their cones. Each has barbs at the end of the scales. The sharp Pinus jeffreyi cone scale barbs point inward, so the cone feels smooth to the palm of one's hand when rubbed down the cone. Pinus ponderosa cone scale barbs point outward, so feel sharp and prickly to the palm of one's hands. This gives rise to the memory device for distinguishing between them - "gentle Jeffrey and prickly ponderosa". Another distinguishing characteristic is that the needles of Pinus jeffreyi are glaucous, less bright green than those of Pinus ponderosa, and by the stouter, heavier cones with larger seeds and inward-pointing barbs. Pinus jeffreyi can be somewhat distinguished from Pinus ponderosa by the relatively smaller scales of bark as compared to the larger plates of more reddish-colored ponderosa bark.
The scent of Pinus jeffreyi is variously described as reminiscent of vanilla, lemon, pineapple, violets, apple, and, quite commonly, butterscotch; This scent may be sampled by breaking off a shoot or some needles, or by simply smelling the resin's scent in between the plates of the bark. This scent is related to the very unusual composition of the resin, with the volatile component made up almost entirely of pure n-heptane.
The largest Pinus jeffreyi, by trunk volume, is the Eureka Valley Giant, in the Stanislaus National Forest. Its trunk contains 4,560 cubic feet (129 m3) of wood, is 192 feet (59 m) tall, with a diameter of 8.1 feet (2.5 m)