Goals from Christian Tue Jensen, Julien Carré and Jaden Brissett ensured the young Bees would return to England having netted nine times in two games and kept two clean sheets.
The young Bees started the game well and went ahead after just 13 minutes when David Titov drove down the right before cutting in and dribbling across the box before he teed up Tue Jensen to sweep a curled effort into the bottom left-hand corner.
The Brentford trialist then had a chance to put himself on the scoresheet when he drove down the left before cutting in and seeing his effort loop up onto the crossbar.
The Russian third tier side would have their first chance midway through the second period with a free-kick from the edge of the Brentford box which threatened Shepperd’s goal, but the powerful effort edged just wide.
The Russian side were then perhaps slightly fortunate not to have been reduced to 10 men when Aleksandr Golovnya slid in high on Gustav Mogensen, but the referee pulled out a yellow card instead of red.
Khabib Abdusalamov would then have a good chance to level when he drove forwards and jinked his way into the box, but for good defending from Japhet Sery Larsen as he managed to prevent him getting a shot away as Shepperd collected.
The away side came out quick after the break with a couple of corners which forced a good block from Nick Tsaroulla.
But Brentford B kept pushing forwards to further their lead and they created two chances when Tsaroulla and Paris Maghoma tricked their way into the box, but neither were able to get a clear attempt away at goal.
Just after the hour mark Brentford B managed to further their advantage and they did it in style when Aaron Pressley made a nuisance of himself to win a header as he beat the Rodina keeper to it, before the ball fell kindly for Carré to half volley sweetly into the top corner.
On 66 minutes, substitute Nikita had a chance to pull a goal back when he was played through one-v-one with substitute Simon Andersson out quickly to deny him.
The high pressing Bees game would pay off again a few minutes later when Carré won the ball high up the pitch before playing in Majka down the right, and he was on hand to cross low for Brissett to tap home to make it three goals in two games for the winger.
With a commanding lead the young Bees managed the game well for the final 20 minutes as they reduced their opponents to little by the way of chances. Late opportunities would follow for Maghoma and Pressley with both having shots blocked as the match finished 3-0.
Brentford B: Shepperd (Andersson, 56), Koutsimouka (O’Connor, 56), Tsaroulla, Read (Hammar, 56), Sery Larsen (Mitchell, 56), Maghoma, Majka, Tue Jensen (Adams, 56), Mogensen (Pressley, 56), Trialist (Brissett, 56), Titov (Carre, 56),
FC Rodina Moscow: Aydarov, Korotkov, Apozyan, Dzhamilov, Golovnya, Filippov, Abdusalamov, Lamanov, Shadrintsev, Volkov, LopatinSubs: Novikov, Levshuk, Khayrulin, Makarov, Tovmasyan, Sukhanov, Nikita, Laktionov