To grow fruit plants, farmers in the Vietnamese Mekong Delta (VMD) must use raised bed constructions to avoid waterlogging during the rainy season. This study aimed to evaluate the effects of the age of the raised beds on the soil physicochemical properties of longan orchards located in the VMD. Two raised bed systems were evaluated: a young bed constructed 10 years ago and an old bed constructed 42 years ago. Soil samples were collected from five different soil layers (0–20, 20–40, 40–60, 60–80, and 80–100 cm) with four replicates per layer. Soil samples were tested for pH, electrical conductivity (EC), available phosphorus (AP), total nitrogen (TN), soil organic matter (SOM), exchangeable cations (Ca2+, K+, Mg2+, and Na+), cation exchange capacity (CEC), bulk density (BD), soil porosity, available water-holding capacity (AWC), particle composition (sand, silt, and clay), and size. The soil pH was approximately 1.0 units lower in the old bed compared to the young bed at depths of 0–20 and 20–40 cm. The BD was higher in the old bed (0.15 g cm−3) than in the young bed at a soil depth of 0.4 m. SOM, AP, exchangeable cations (Ca2+, Na+, and Mg2+), AWC, and soil porosity were significantly lower in both the topsoil (0–20 cm) and subsoil (20–40 cm) layers in the old bed than in the young bed. In particular, the SOM, AP, AWC, and soil porosity contents in the old bed decreased by 18%, 20%, 15%, and 17%, respectively, compared with those in the young bed at soil depths of 0–40 cm. Therefore, cultivating raised bed soil for a longer period significantly reduced the soil exchangeable cations, porosity, and fertility of the surface and subsurface soils. Based on these results, farmers should use soil conservation practices, such as cover crops, rice straw mulching, and soil amendments in their orchards to mitigate topsoil degradation.