Dear Ramesh,
Your problem seems like you have contamination in your mobile phase A solvent (aqueous phase). The impurities build up in the column while the gradient programme runs at low organic, and subsequently they are eluted out of the column when the gradient programme hits the higher % of mobile phase B (organic phase).
Try to run your separation with fresh batch of aqueous phase or track any step in the preparation of the mobile phase where you might be putting contaminants (buffers salt quality, pH measurement of the aqueous phase, filtering etc.)
By the way, what is the composition of your mobile phase? Are you running RP chromatography? At which type of column?
Regards