The Hornets are preparing for their FA Cup semi-final against Crystal Palace at Wembley on Sunday but the boss does not believe his side will be weakened because of the changes.
Flores said: "We will respect the shape, we are not going to change a lot because we have been playing with the same system, or very similar, for some time but in terms of the players they know we will change a lot.
"We will use a lot of new players (against West Ham).
"I am completely confident in the first XI I will pick tomorrow, I am really curious how we can develop, and the characteristics of the players.
"I think it will be very interesting to know.
"We respect West Ham, they are very good, they are one of the best in the Premier League but I trust a lot in my players and I think we can give a very good performance."
Despite not being mathematically safe from the drop, Watford look a good bet to retain their top-flight status and Flores is keen to finish on a high as well as progress in the FA Cup so they can develop next season.
He said: "The most important game is the next one
It is impossible to think that it is not a difficult one (against West Ham).
"We would play at risk if we think about the weekend so it is very important to focus on West Ham.
"Our objective was always the points, to go up in the league and try and improve every time but there are a lot of teams trying to do their best.
"I think we are in a position where we can finish in a really good position in the league.
"41 points is really good in the first year you are promoted and we are happy but we can do more.
"We are not going to change the idea, we are working how we want with our philosophy so we will keep working.
"Our confidence is (great) and we are really excited to see how they players do."
West Ham are sixth in the league and the Hornets boss is not surprised at their success this season, despite beating them 2-0 when the sides first met in October.
Flores said: "West Ham have amazing wingers, amazing players in the middle
They are one of the best teams in the Premier League.
"They look really good since we won in an amazing match at the beginning of the season.
"We analysed then and we have analysed now again and they have progressed.
"It is an amazing stadium and a very tough challenge so it is an amazing opportunity for those who play.
"They are one of those teams who always progress because the coach manages well and the players are really, really good.
"For me it is no surprise they are in the top five or six in the Premier League."
Source : PA
Source: PA