Continuous quantum measurement is the backbone of various methods in quantum control, quantum metrology, and quantum information. Here, we present a generalized formulation of dispersive measurement of a complex quantum systems. We describe the complex system as an open quantum system that is strongly coupled to a non-Markovian environment, enabling the treatment of a broad variety of natural or engineered complex systems. The system is monitored via a probe resonator coupled to a broadband (Markovian) reservoir. Based on this model, we derive a formalism of Stochastic Hierarchy Equations of Motion (SHEM) describing the decoherence dynamics of the system conditioned on the measurement record. Furthermore, we demonstrate a spectroscopy method based on weak quantum measurement to reveal the non-Markovian nature of the environment, which we term weak spectroscopy.Introduction -Generalized or weak quantum measurement has become increasingly important in the last decade due to its application in quantum feedback control [1, 2], quantum metrology [1], quantum information [3][4][5], and the study of quantum-classical transitions [6,7]. The existing theories consider continuous weak measurement of simple open quantum systems with Born-Markov decoherence models [5,[8][9][10]. However, there is a lack of theoretical formalism to extend the exceptional capacities of weak measurement method for system identification and control to complex natural [11] or engineered [12,13] systems, i.e., systems that are large, possibly disordered and interacting strongly with their environment. The present letter addresses the demand for such advanced theories.Cavity quantum electrodynamics (CQED) is a well established paradigm to implement weak quantum measurement protocols [5,8]. In this paper, we develop a CQED theory for continuous measurement of an arbitrary quantum system coupled to a bosonic environment. In this framework, we derive a set of coupled stochastic differential equations, SHEM, that describes the system conditional evolution in the presence of non-Markovian and possibly strong decoherence effects. As an application of our theory, we propose a simple experimental spectroscopic procedure to diagnose the non-Markovian nature of the decoherence dynamics via continuous measurement. Our theory can be applied in any frequency regime, given the appropriate parameters setting. We shall therefore use the term CQED to refer to both cavity (optical) and circuit (microwave) QED systems.We should emphasize that the current SHEM formalism describes a different measurement paradigm than the measurement interpretations of non-Markovian stochastic Schrödinger equations [14][15][16][17][18][19]. The latter, originally developed to model decoherence dynamics in presence of a bosonic environment [14][15][16][17], under certain conditions, describe direct monitoring of the environment [18,19]. In the measurement setting considered in this letter, we avoid such a direct environmental monitoring, rather we use an independent cavity coupled to a...