Well, the main reason was that Lithuanians, unlike Prussians, Latvians or any other Balts, managed to create a country. While the Teutonic knights occupied Prussia and fought with them, Lithuania started to steadily create a country. Most historians agree, that it was formed around the year 1240. So some sort of organization, combined with effective attack and defence tactics(Lithuanians often fought in swamp lands or forests rather than open field, where the Teutons couldn't effectively use their heavy armor and horses. Mostly hit and run tactics were used) and difficulty for the Knights to establish themselves in other occupied lands let Lithuania form itself politically.

Then, when Lithuania became a Christian kingdom for a while(from 1253), there was a truce and we had the opportunity to further develop the country. But that didn't last long, as our King Mindaugas resumed fighting with Christians in 1261 and returned to the old religion.

A few decades after his death, Lithuania started to heavily expand it self towards Ruthenian lands, sometimes taking land by force, sometimes through marriages and alliances. That gave the country even more allies and manpower to successfully defend itself for more than 100 years until finally christianizing for good and together with Poland, curbing the Teutonic orders influence in the region after the battle of Grunwald(or Žalgiris in Lithuanian). An important thing to add would be that because of the necessity of it, Lithuania largely based almost everything it had into it's military, expanding it and building more castles, forts and expanding the territory to places of strategic importance.