1st trade - I am buying 1000 shares of X @ 250 and sells @ 251, here i understand that the brokerage is 40 rs (including buy and sell).

2nd trade in a same day - buy 200 shares of X @ 249 and sells @ 250, what will be the brokerage either 10.02 or 40 rs. In a simple way is that 0.01% brokerage is applicable to that particular order turnover or a days total turnover.

Simple, every executed order is Rs. 20/- (BUY - 20/- plus SELL 20/-), so total Rs. 40/- for your first BUY/SELL. Similarly, your second BUY/SELL is also Rs. 40/-

So, total brokerage is Rs. 80/- for the full day.

(P.S. I have not considered STT, Service Tax, Cess…etc)

1st trade - I am buying 1000 shares of X @ 250 and sells @ 251, here i understand that the brokerage is 40 rs (including buy and sell).

Agreed. Brokerage is 40. Your understanding is correct.

2nd trade in a same day - buy 200 shares of X @ 249 and sells @ 250, what will be the brokerage either 10.02 or 40 rs. In a simple way is that 0.01% brokerage is applicable to that particular order turnover or a days total turnover.

Yes. You are right. 0.01% brokerage is applicable for every separate order's turnover. Not for the entire day's turnover. So you will be charged (249+250) x 200 x 0.01% = 9.98 for this second trade. Note: For Intraday, your single order includes both Buy and Sell, so you need to add 249x200 and 250x200 together and see that as your turnover for brokerage purpose.