Thursday's court proceedings follow two months of pre-trial hearings.
Chen has denied the charges, saying the administration of Ma Ying-jeou, the current president and Chen's succesor, is "persecuting'' him "to gain favours and protection from the Beijing authorities".
Chen stepped down last May after completing his eight-year presidency.
The case has skewed public opinion of Taiwan's opposition Democratic Progressive Party (DPP), which backed Chen when he was in office.
He left the DPP in August.
The case has also deepened differences between those who support a more pro-independence stance for Taiwan as Chen did, and those who seek warmer ties with China as Ma Ying-jeou has done.
China, which still considers Taiwan a renegade province and has threatened to use force to quell any move towards formal independence, often bristled at Chen's independence moves.
The two neighbours have enjoyed a thawing of relations since Ma won elections last year on a platform of having closer relations with Beijing.