Natural resource evaluation is a prerequisite for the rational utilization of natural resources. Compared with traditional monitoring and assessment approaches, the evaluation of natural resources in highly urbanized zone should emphasize the holistic assessment of components and interactions within socio-ecological systems. From the perspective of full-element and full-cycle management of natural resources, this study introduces adaptive cycle theory to address the resource endowments and refined management characteristics of urbanized zone. A comprehensive evaluation indicator system is developed using methods such as the CRITIC weighting approach and multi-indicator comprehensive evaluation, with Shanghai as an empirical case to support optimized natural resource governance. The results demonstrate that: (1) Compared to traditional monitoring frameworks, this indicator system provides a novel theoretical lens for evaluating natural resources in urbanized zone, better reflecting human-nature interactions within resource systems. (2) From 2006 to 2020, Shanghai exhibited improvements in three dimensions—resource potential, ecological resilience, and spatial connectivity. All districts remained in the development-conservation transitional phase, highlighting the urgent need to integrate the conservation and development of diverse natural resource elements and spatial categories.