After the HKU governance reform of 2003, Prof. Kwok was one of the first 10 new executive deans appointed with human resources and budgetary responsibilities to implement a host of administrative changes.  At the same time, the University had ambitious plans to reform the curriculum, increase both the undergraduate and postgraduate student population, and a major recruitment drive for new academic staff.   During his 10-year tenure as Dean of Science from 2006 to 2016, Prof. Kwok implemented the new University policies of mapping from the British academic titles to American ranks, an annual performance review system (resulting in variable pay), a new tenure and promotion procedure, a new rigorous hiring procedure, and the introduction of the Common Core curriculum. 

At the Faculty level, Prof. Kwok initiated a number of curriculum and governance reforms. These include replacing the old rigid programs by a flexible major/minor system in 2006, Faculty common admission for greater student choice in 2007, experiential learning requirements in 2007, academic advising system in 2007, integration of the former Botany, Ecology, and Zoology departments in to a single School of Biological Sciences in 2007, introduction of a new interdisciplinary major Environmental Science in 2008, academic induction in 2008, introduction of undergraduate summer research fellowship and overseas research fellowship in 2008, and the offerings of science service courses for engineering and medicine students in 2012.

A highlight of the science curriculum reform is the first-year core sequence of new science foundation courses, which he designed with the help of a group of dedicated teachers. These Science Foundation courses, together with the rationale and implementation of the curriculum reform, are described in an article in an article in Nature Astronomy.

Prof. Kwok has also aggressively recruited new academic staff from overseas. Between 2006 and 2016, he has successfully recruited international staff from a wide variety of countries, including Australia, Canada, Finland, France, Italy, Japan, Korea, Singapore, South Africa, Switzerland, Taiwan, U.K., and the U.S.A. As a result, HKU Science is among the most diverse academic institutions in this part of the world. International collaboration is now the norm in the Faculty of Science. Some of these activities were reported in the magazines Science (September 2012) and Physics Today (Dec 2012).