I'm assuming you know about EVs since you're training in the Secret Base...
Your Raikou is gaining Sp. Attack EVs. Since it is LV 50 and has not gained any EVs yet, you will see a large initial raise in Sp. Attack, since the game has to recalculate your Pokemon's stats, so that it's as if your Raikou has been gaining EVs all its "life."
Then you will start to see lower gains in Sp. Attack, since the FULL stat gain from EVs is only seen once your Pokemon is at LV 100--it adds up gradually. Your Raikou is STILL gaining the same EVs, and it will have all the Sp. Attack it's supposed to once it's at LV 100.
Please ask all further EV-related questions in the sticky, and I know you're not from the US, but trying to phrase your questions a little more clearly would be REALLY helpful.
-Answered, closed