As the other answer and comments pointed out, all three Baltic states fought to resist the Soviet re-occupation after 1944. The Lithuanian effort were relatively more determined, costing the Lithuania about as many lives as the rest of the Baltic resistances. More importantly, however, during this period Lithuania was slower in its economic development compared to both Estonia and Latvia, as a result of reduced investment levels.
After 1945, the Soviet Fourth Five Year Plan provided the next lowest level of investment per capita in Lithuania of all the Soviet republics. The rate of industrial growth in Lithuania in the 1940s and early 1950s was much slower than in Estonia and Latvia.
- Lane, Thomas. Lithuania: Stepping Westward. Routledge, 2014.
Gresh demands for industrial labour were thus largely sufficiently met by local ethnic Lithuanians. The resulting lack of economic need or opportunity helped reduce prospective Russian settlements.
The resistance movement, slower rates of industrial development, helped restrain the massive migration of Russian settlers to Lithuania which the Estonians and Latvians experienced ... [Because Lithuania] could provide manpower for the new Soviet enterprises, Russian settlement was minimized.
- Dawisha, Karen, and Bruce Parrott. The Consolidation of Democracy in East-Central Europe. Cambridge University Press, 1997.
Furthermore, the Lithuanian situation benefited from a greater autonomy and better relations with Moscow that its Lithuanian Communist Party enjoyed. This allowed the Lithuanian party to retain a stronger national character relative to the other Baltic states. Lithuania was thus able to weather the purge of Baltic nationalism that Moscow instituted when Latvia tried to stem the tide of Russian immigration.
Even the purge of Lithuanian 'national communism' which took place in 1959 was mild by comparison with comparable purges in Estonia and Latvia and did not affect the position of the first secretary ... There were more native communists in the Lithuanian Communist Party than in any other republic apart from Armenia and Georgia.
- Hiden, John, and Patrick Salmon. The Baltic Nations and Europe: Estonia, Latvia and Lithuania in the Twentieth Century. Routledge, 2014.
Lastly, native Lithuanians bred abundantly under the Soviet occupation. Both Latvia and Estonia saw a reduction in their national majority due to a slow birth rate - Latvians increased by only 3.4% from 1959 to 1970. In contrast, the native Lithuanians outbred the Russian settlers with double digit growth over the same period.
There were 2,507,000 Lithuanians in Lithuania in 1970, which was a gain of 16.5 percent over the 1959 figure of 2.151.000. They even managed to improve their majority in the country's total population from 79.3 to 80.1 percent.
- Szporluk, Roman. Russia, Ukraine and the Breakup of the Soviet Union. Hoover Press, 2000.
Incidentally, at ~80%, Lithuania was the most ethnically homogeneous of the Baltic states to begin with, compared to Latvians at ~60% and Estonians at ~70%.