PhD graduates play an important role in the national innovation system. However, only a few studies have explored Chinese PhD graduates' employment and development prospects because of limited data. To fill in this gap, this study conducted a survey of doctoral recipients in 13 Chinese universities. The authors drew on the national survey data and in-depth interviews to critically analyze the PhD graduates' job preferences, employment outcomes, and factors that affect their employment sectors. Results indicate a notable difference between the graduates' job preferences and their employment outcomes. The proportion of employment in academia is substantially below expected, particularly among female graduates. This study specifically focuses on the impact of gender and scientific output (including articles and patents) on the employment outcomes of PhD graduates. Compared with graduates employed by the non-academic sectors, male graduates have a lower probability of employment in universities and research institutions. Compared with those working in enterprises, PhD graduates employed in universities and research institutions published more during their doctoral study. For graduates who majored in science, engineering, and agricultural sciences, having patents increases their probability of working in the enterprises.