I am afraid there is no flight from Indian to Nanjing. You's better get to Shanghai first and then take airport shuttle bus to Shanghai Train Station. You can take bullet train to Nanjing at the train station. It is fast and comfirtable. You can get into Nanjing 2.5 hours later (about 4 hours by bus).

If Shanghai is not part of your itinerary, it is easier to get to Nanjing with a connecting flight through Beijing or Tokyo. Shanghai's two airports are many miles apart, and it often takes over an hour to transit between. If you overnight in Shanghai, your best bet is the frequent, fast, and modern train service to Nanjing.