The ecological compensation mechanism emerges as a solution to reduce pollution for aquatic product supply chain. To comprehend the dynamic pollution management strategies and coordination under the ecological compensation mechanism, this study develops a stochastic differential game between farmers and firms from the perspective of extreme weather crisis. The subjects’ optimal decisions are explored in three cases including cooperative case, noncooperative case, and land transfer-cost sharing contract case. Then we simulate theoretical results and illustrate a case study to demonstrate the applicability of ecological compensation collaboration. The results indicate that the extreme weather crisis changes the evolutionary trend and steady state of pollution accumulation. Moreover, the land transfer-cost sharing contract could realize the Pareto improvement in high-risk environment especially after the crisis. But its coordination relies on the ecological compensation coefficient, which gets larger with the interval of [4.9,6.3] after the crisis, compared to the range of [4,5.4] before the crisis. Notably, the contract and ecological compensation mechanism exhibit a complementary relationship in response to the crisis. The findings could provide new inspirations for aquatic product supply chain to balance production and environmental protection.