My understanding is that it was to do with control over Korea and Manchuria.
I have a couple of questions:
The immediate cause was Russia's occupation of Manchuria after the Boxer Uprising. Japan saw the Russian presence as a threat to her own economic ambitions in the area as well as a menace to her position in Korea. Negotiations in 1902-03 produced agreement for phased withdrawal, but Russia reneged on the second stage. Russia's main disadvantage was the remoteness of the war theatre from her main centres of population, production and military & naval concentration: the newly-completed Trans-Siberian Railway remained mostly a single track, and the Baltic fleet took seven months to reach the area before sinking under superior Japanese gunnery. Manchuria was certainly rich in agricultural and mineral resources, and had only recently been opened by the Qing court to Han Chinese settlement, making it attractive for colonisation by others too. Victory catapulted Japan into the ranks of the powers and brought commercial dividends from trade and investment: by the 1930s Manchuria (now under direct Japanese domination) became one of China's most productive regions. For Russia, the political consequences were dramatic, with revolution forcing the Tsar to grant a constitution and national assembly in 1905, but economic and military recovery were rapid after 1908, prompting German fears and contemplation of a pre-emptive war.