INTRODUCTION: Hypertension (HT) and diabetes mellitus (DM) and are major disease burdens in all healthcare systems. Given their high impact on morbidity, premature death and direct medical costs, we need to optimise effectiveness and cost-effectiveness of primary care for patients with HT/DM. This study aims to find out the association of trajectories in disease patterns and treatment of patients with HT/DM including multimorbidity and continuity of care with disease outcomes and service utilisation over 10 years in order to identify better approaches to delivering primary care services. METHODS AND ANALYSIS: A 10-year retrospective cohort study on a population-based primary care cohort of Chinese patients with documented doctor-diagnosed HT and/or DM, managed in the Hong Kong Hospital Authority (HA) public primary care clinics from 1 January 2006 to 31 December 2019. Data will be extracted from the HA Clinical Management System to identify trajectory patterns of patients with HT/DM. Complications defined by ICPC-2/International Classification of Diseases-Ninth Revision, Clinical Modification diagnosis codes, all-cause mortality rates and public service utilisation rates are included as independent variables. Changes in clinical parameters will be investigated using a growth mixture modelling analysis with standard quadratic trajectories. Dependent variables including effects of multimorbidity, measured by (1) disease count and (2) Charlson's Comorbidity Index, and continuity of care, measured by the Usual Provide Continuity Index, on patient outcomes and health service utilisation will be investigated. Multivariable Cox proportional hazards regression will be conducted to estimate the effect of multimorbidity and continuity of care after stratification of patients into groups according to respective definitions. ETHICS AND DISSEMINATION: This study was approved by the institutional review board of the University of Hong Kong-the HA Hong Kong West Cluster, reference no: UW 19-329. The study findings will be disseminated through peer-reviewed publications and international conferences. TRIAL REGISTRATION NUMBER: NCT04302974.