Milan Malpensa train to Florence

You need take the Malpensa Express to Milan Centrale.
And then take Milan Centrale to Florence.

best train website:
http://www.trenitalia.com/

When searching this site you need to use the Italian spelling of the city you want to go to.
e.g.
Milano Centrale to Firenze Santa Maria Novella

You can buy a ticket to Firenze Santa Maria Novella at the airport train station; you will change at Milano Centrale. Very easy, all tracks are on one level, no stairs to change trains. You may be issued two tickets. Trenitalia is the website but I would not purchase tickets online ahead of time in case your flight is delayed.

If you haven't travelled in Italy before, here's a brief summary of the route to follow if arriving in Milan....

TRAVEL FROM MILAN / MXP TO MILANO CENTRALE
The quickest and easiest way to get from MXP Terminal 1 into Milan is to use the Malpensa Express (train). There are several departures each hour and the trip takes 52 minutes. You can buy tickets at the airport station either from a Kiosk or staffed ticket office, and the cost is currently €13 PP. There are a few important points to note. First, the M.E. has two routes, one to Milano Centrale and one to Milano N. Cadorna, so be sure to board the correct train! Next, it's necessary to validate (time & date stamp) your tickets prior to boarding the train, or you'll risk hefty fines which will be collected on the spot! You'll arrive at Milano Centrale on Track (Binario) 1 or 2, and will then have to walk into the main hall to either connect with another train or exit the station.
If you're arriving on a budget flight at Malpensa Terminal 2, you can use either the Malpensa Shuttle (Bus) or the Malpensa Express (train). Travel time for the bus is about an hour (depending on traffic), and the Bus also terminates at Milano Centrale. Travel time for the train is a bit longer than from Terminal 1. You can buy bus tickets from the driver or at ticket machines inside the terminal. The Malpensa Shuttle also serves MXP Terminal 1, so if you'd prefer to travel by Bus that's also an option.

It's generally recommended by most here that tickets for the express (high speed) trains (Milan to Florence) be purchased AFTER you arrive in Italy. You should be able to buy your ticket for the train from Milano Centrale to Firenze SMN at the airport. You could also wait until you arrive at Milano Centrale and buy from a Kiosk. The reason for not buying an advance ticket, is that if your flight is late and you miss the train you've booked, the ticket is worthless and you'll have to buy another anyway.

The direct trains that did not require a connection on that route were few and short-lived.