Rubber plantations have rapidly replaced natural forests (NFs) in Mainland Southeast Asia, yet the relevant impacts on the terrestrial carbon cycle remain uncertain especially with an increase in drought frequency. Our study compared eddy-covariance measurements of carbon and water fluxes from two rubber monoculture plantations (at a northern marginal site and a southern traditional plantation site) with a second-growth NF between 2015 and 2018, and their responses to a prolonged drought during 2015/2016. The NF had higher light use efficiency, water use efficiency and gross primary productivity (GPP, 2.94 ± 0.41 kg C m−2 yr−1) than the northern rubber (NR) monoculture (2.45 ± 0.17 kg C m−2 yr−1), while lower ecosystem carbon use efficiency (eCUE) caused a lower net ecosystem productivity (NEP, 0.75 ± 0.25 kg C m−2 yr−1) compared to the plantation (1.19 ± 0.22 kg C m−2 yr−1). Drought decreased the NF eCUE by 23% with significant carbon uptake restrictions across multiple seasons, while the rubber GPP reduction was only substantial in the warm-dry season with an overall 17% decline in eCUE. The NR site's GPP was mainly controlled by soil water content throughout the year. Higher light availability offset the negative effect of drier conditions on the rubber GPP, resulting in larger carbon uptake compared to the southern plantation (GPP, 2.12 ± 0.12 kg C m−2 yr−1; NEP, 1.07 ± 0.14 kg C m−2 yr−1). In contrast, the NF GPP was mainly restricted by vapor pressure deficit, especially during the drought.