Complex systems in the intelligent era are characterized by multi-domain interconnection and deep integration of human, machine, and things. Operating in open, dynamic, and even adversarial environments, these systems are exposed to multi-dimensional disturbance threats, posing severe challenges to their survivability and usability. To address the limitations of classical systems engineering theories and methods in handling uncertainties and sudden disturbances, this study proposes a concept of resilience systems engineering and constructs its methodological framework. It explores the paradigm of "built-in resilience design" during the system design phase, aiming to enhance the continuous operation, adaptive, and evolutionary capabilities of complex systems. Moreover, the study sorts out the multidisciplinary definitions of resilience, clarifies the classification of disturbance factors and the division of resilience capability phases, and compares the differences between resilience and other related concepts such as fault tolerance, survivability, security, and robustness. On the basis of classical systems engineering theories and methods, this study introduces the theoretical elements of resilience, proposes the concept and methodological process of resilience systems engineering, and integrates resilience capabilities (including prevention, resistance, adaptation, recovery, and evolution) into the full lifecycle design of systems. A resilience measurement framework is established, which covers both general indicators and domain-specific indicators, and consists of quantitative and qualitative evaluation dimensions. Taking the autonomous cruise robot system as a case study, the study elaborates on the application process of the resilience systems engineering method. Focusing on typical fields including power energy systems, information and communication networks, unmanned intelligent systems, and supply chain networks, this study discusses the engineering exploration of resilience theories and methods, and further analyzes the challenges faced in their practical implementation. Through continuous theoretical innovation, methodological improvement, and engineering practices, resilience systems engineering is expected to evolve into a new paradigm of systems engineering, providing solid theoretical and methodological support for the safe, reliable, and continuous operation of critical infrastructure, intelligent unmanned equipment, and complex systems.