Matsumoto station is the main station of Matsumoto city in Nagano prefecture. Matsumoto is the second populated city in Nagano, after the prefectural capital, Nagano city. Actually these two cities are in same prefecture but two different regions and have a big rivalry. Nagano is the capital but national university is located in Matsumoto. Nagano has the well known temple, Zenkoji but Matsumoto has the national treasure castle. Then, Matsumoto has the airport but Nagano has Shinkansen station.
Therefore Matsumoto is more academic city than Nagano which is more business and political city. Also Matsumoto is the gateway for popular Kamikochi and other nature and mountain areas.
The best way to reach Matsumoto station from Tokyo is to take limited express Azusa or Super Azusa, which departs from Shinjuku station. If you are staying close to Tokyo or Ueno stations, and if you do not mind changing trains, take Hokuriku Shinkansen to Nagano and change to limited express Shinano. The journey time is almost the same.