This medium-large, dark brown eagle is stocky, with rounded wings and a short tail. Its short black and white fan-shaped nuchal crest gives it a thick-necked appearance. The bare facial skin and feet are yellow. The underside is spotted with white and yellowish-brown. When perched the wing tips do not reach until the tail tip. In soaring flight, the broad and paddle-shaped wings are held in a shallow V. The tail and underside of the flight feathers are black with broad white bars. Young birds show a lot of white on the head. The tarsus is unfeathered and covered by hexagonal scales. The upper mandible does not have an overhanging festoon to the tip.
This species of serpent eagle manifests an unusual amount of size variation across its assorted subspecies. Total length of fully-grown crested serpent eagles can vary from 41 to 75 cm (16 to 30 in) and wingspan can vary from 89 to 169 cm (2 ft 11 in to 5 ft 7 in). The largest proportioned race appears to be the nominate, S. c. cheela, with a wing chord of 468 to 510 mm (18.4 to 20.1 in) in males and 482 to 532 mm (19.0 to 20.9 in) in females, tail lengths of 295 to 315 mm (11.6 to 12.4 in) and tarsus length of 100 to 115 mm (3.9 to 4.5 in). In comparison, S. c. minimus, probably the smallest race, has a wing chord of 257 to 291 mm (10.1 to 11.5 in) in males and 288 to 304 mm (11.3 to 12.0 in) in females, tail lengths of around 191 mm (7.5 in) and tarsal length of around 76 mm (3.0 in). Weights are more fitfully reported but are estimated to vary perhaps threefold between assorted races. In very small subspecies such as S. c. asturinus body masses were found to be 420 g (15 oz) in a male and 565 g (19.9 oz) in a female. In S. c. palawanesis, body mass was reported at 688 g (24.3 oz) in males and 853 g (30.1 oz) in females.
Serpent eagles from Borneo, S. c. pallidus, may between 625 and 1,130 g (22.0 and 39.9 oz). Mainland forms are typically larger but a weight of 900 g (32 oz) was cited for the fairly small mainland race, S. c. burmanicus. In the race S. c. hoya, weights were much higher, averaging 1,207 g (42.6 oz); meanwhile, in the same race, 8 males averaged 1,539 g (54.3 oz) and 6 females averaged 1,824 g (64.3 oz). In some cases, serpent eagles may attain estimated weights of approximately 2,300 g (81 oz).