During the past two decades, the Maritime Continent (MC) has experienced increased deforestation1,2. Using hundred-year long ensemble idealized deforestation experiments conducted with the fully-coupled Community Earth System Model (CESM) V1.2, here we show that the MC deforestation have a potential to alter the complexity (i.e., event-to-event differences) of the El Niño-Southern Oscillation (ENSO) in terms of its spatial pattern and temporal evolution. The deforestation model run increases the occurrences of Central Pacific El Niño and multi-year La Niña events compared to the control experiment. This change in ENSO complexity is caused by the strengthening effect of MC deforestation on subtropical ENSO dynamics. Conventional tropical ENSO dynamics influence ENSO occurrence and evolution through variations in the tropical Pacific thermocline and related tropical ocean-atmosphere interactions. However, subtropical ENSO dynamics govern the ENSO through coupling processes originated from the subtropical North Pacific. The MC deforestation in our idealized experiment accompanies an anomalous local overturning, which further alters the mean strength of the North Pacific subtropical high and strengthens subtropical ENSO dynamics. Therefore, MC deforestation has the potential to make the El Niño more complex and less predictable.