He finished 2.8 points ahead of Germany's Severin Freund with Japanese Taku Takeuchi third.
Kot, who won the first of the nine summer events in Wisla in July 21, had jumps of 87.5m and 88.5m.
Germany's Andreas Wank was only 11th but holds a 87 point lead over Slovenian Jurij Tepes going into Wednesday's final round in Klingenthal.
Gregor Schlierenzauer and Thomas Morgenstern were fifth and seventh respectively as the top Austrians returned to action after taking the summer off.
1 Maciej Kot (Poland) 230.1 (87.5m & 88.5m)
2 Severin Freund (Germany) 227.3 (87.5m & 89.0m)
3 Taku Takeuchi (Japan) 227.2 (88.0m & 88.5m)
4 Anders Fannemel (Norway) 225.5 (95.5m & 90.0m)
5 Gregor Schlierenzauer (Austria) 224.6 (88.0m & 88.0m)
- Sports & Recreation
- Severin Freund
- Gregor Schlierenzauer
- Taku Takeuchi
- Andreas Wank