The leaves of japanese clover are alternately arranged and compound, with each trifoliate leaf comprising three leaflets. These leaflet blades are broadly oblong-elliptic to oblong-obovate, measuring 0.5-1 inch (1.3-2.5 cm) in length and approximately one-third to one-half as wide. The leaf margins are smooth and entire, and the leaflets' surfaces are typically green with a smooth texture. This trifoliate arrangement and distinct oblong shape are key identifying features.

Japanese clover features small, 1/4 inch (6 mm) long flowers that bloom in groups of 1-3 within the leaf axils. Each flower has a distinctive shape similar to pea flowers. The lower petal is pink or purple, while the two smaller upper petals are white. These flowers can either be upright or horizontal. They bloom in mid-summer, typically lasting for 1-2 months. The petals' arrangement and vibrant colors make these flowers easily identifiable.

The stems of japanese clover are purplish in color and feature a prominent covering of appressed white hairs that point downward. These hairs give the stem a distinctive texture, making it slightly rough to the touch. The stems are slender and exhibit a creeping or sprawling growth habit, typically reaching lengths of up to 1 foot (30 cm). Branching occurs frequently, creating a dense mat of interwoven stems. This characteristic stem morphology aids in the plant's identification.

The fruit of japanese clover is a small, elongated legume, roughly 0.2 inch (5 mm) in length. Encased within a discreet, hair-lined pod, the fruit bears a signature single seed. Upon maturity, the pods exhibit a tan to brown hue, boasting a texture that transitions from initially soft to a more hardened, dry state. These diminutive fruits present a smooth surface, with a visible seam running longitudinally, which splits open upon seed dispersal. The simplicity of the fruit, while modest in ornamentation, is distinctive in its solitary-seeded presentation.