This volume contains the proceedings of the Conference on Analysis, Complex Geometry and Mathematical Physics: In Honor of Duong H. Phong, which was held from May 7-11, 2013, at Columbia University, New York. The conference featured thirty speakers who spoke on a range of topics reflecting the breadth and depth of the research interests of Duong H. Phong on the occasion of his sixtieth birthday. A common thread, familiar from Phong's own work, was the focus on the interplay between the deep tools of analysis and the rich structures of geometry and physics. Papers included in this volume cover topics such as the complex Monge-Ampere equation, pluripotential theory, geometric partial differential equations, theories of integral operators, integrable systems and perturbative superstring theory.