To protect forest land from loss and mitigate the global climate crisis, China has proposed a stringent natural forest protection plan, known as China’s natural forest logging ban (NFLB). This policy aims to halt the over-exploitation of natural forests, restore forest ecosystem functions, and promote regional green economic development. This study uses a regression discontinuity design (RDD) model to quantitatively and comprehensively assess the effectiveness of this policy in the key state-owned forest regions in Northeast China. Additionally, it analyzes the heterogeneity and structural characteristics of the policy’s effects on the internal composition of ecological and economic systems. The empirical results are as follows: (1) Ecological and economic impacts: The policy has successfully achieved its ecological objectives by significantly enhancing the quality and value of ecosystem services. However, it has also had a notable adverse impact on economic development, particularly in the timber supply sector, reducing the conversion efficiency of ecosystem service values into economic benefits. (2) Structural analysis: The logging ban effectively promoted the value of various ecosystem services, particularly enhancing regulatory and support functions, with a LATE estimate of approximately 8.47 units. The implementation of the policy caused a negative growth in the output value of supply-oriented ecological products, and the significance level was lower than 0.1. Conversely, the LATE estimates for different types of GDP indicate a negative growth in supply-type GDP due to the policy, with p < 0.1. (3) Heterogeneity: On the one hand, a simplistic and singular approach to logging prohibition may constrain the efficiency of enhancing ecosystem service values. On the other hand, although the policy disrupted the majority of traditional forest enterprise operations, business models focusing on quality and technology improvements were able to mitigate this impact.