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Chasing 242 for victory, New Zealand lost their final seven wickets for 43 runs to lose by 123 runs. England won the opening game by 142 runs.
Skipper Suzie Bates (24) and Maddy Green (20) were the only New Zealand players to reach 20.
Tami Beaumount (67 from 76 balls) top scored for England as they were bowled out for 241 in 48 overs. Natalie Sciver scored 54 for her 10th ODI half-ton.
Sophie Devine, Leigh Kasperek and Jess Watkin all took two wickets each.
The third and final game takes place in Leicester on Saturday.