This paper proposes a novel framework for multi-objective optimization of photonic crystal (PhC) filters and compares it with a single-objective optimization approach. In this framework, an optimizer called the Multi-Objective Gray Wolf Optimizer has been utilized to automatically find the optimal designs. The proposed method is able to design any kind of PhC filter. As a case study, a new structure of super defect PhC filter for application in the wavelength-division multiplexer (WDM) is designed using the framework. The results show that the proposed framework is comprehensive and able to find a significantly wide range of optimal designs for general and specific application, such as WDM with respect to each defined WDM standard.