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The aim of the study was to assess the effects of the maternal and child health (MCH) system strengthening through multilevel governmental collaboration in Nujiang Prefecture, China. A case study design was applied. Guided by the logical framework of the Nujiang MCH Comprehensive Intervention Project, national, provincial, and prefecture government sectors jointly implemented comprehensive health system strengthening (HSS) interventions in Nujiang Prefecture. In this case study, we conducted the end point surveys (November 2015 and January 2016) with 33 local MCH facilities. We also interviewed 35 MCH providers, government officials, leaders of MCH facilities, and project specialists. The thematic framework method was used to analyze the interview data, and descriptive analysis was performed to analyze the survey data. The three levels of governmental collaboration contributed to increased government investment in the local MCH system and ensured the successful implementation of the project. Participatory training methods and appropriate HSS interventions tailored to the local context were crucial to improve MCH providers' knowledge and skills, with the proportion of qualified MCH providers increasing from 70% in 2011 to 96% in 2015. Owing to this increase in knowledge and the increase in needed equipment, more MCH hospitals could provide inpatient obstetric services, and more town health clinics were capable of providing basic MCH services. The development of a reimbursement policy tailored to the local context promoted in-hospital delivery. At the conclusion of the project, percentages of antenatal care, in-hospital delivery, and newborn screening increased by 20.71%, 18.12%, and 278.62%, respectively. Growth monitoring coverage for children younger than three years remained stable at around 90%. However, the MCH system was negatively impacted by the workforce shortage. Those shortages were caused by a lack of positive recruitment and retention and incentive policies. Implementation of comprehensive HSS interventions through multilevel governmental collaboration improves the MCH system in remote and low-income areas. • Multilevel governmental collaboration improves the Maternal and Child Health (MCH) system in remote and low-income areas. • Participatory training methods contributes to the positive effects of health system strengthening interventions. • The MCH system is negatively impacted by the workforce shortages and inadequate incentives for health providers. [ABSTRACT FROM AUTHOR]