Purpose To evaluate the availability, cost, affordability, and drug utilization of anti-cancer medicines in Nanjing, Jiangsu.Methods Based on the standard survey methods of World Health Organization/Health Action International(WHO/HAI), a longitudinal tracking investigation study was performed to collect information about 24 essential anti-cancer medicines (EAMs) and 17 innovative anti-cancer medicines (IAMs) in 26 healthcare institutions in Nanjing from 2016 to 2020. The availability, defined daily dose cost (DDDc), defined daily doses (DDDs) and affordability of EAMs and IAMs were investigated. Wilcoxon’s rank-sum test was used to analyze the available data of adjacent years to check whether there was a statistical difference.Results The availability of EAMs during the study period showed no significant changes in Nanjing, but the availability of IAMs showed a significant increase in 2018 and 2019 and tended to stabilize in 2020. For EAMs, the DDDc of lowest-priced generics (LPGs) showed no significant changes during the study period, and the DDDc of originator brands (OBs) and IAMs significantly decreased. The DDDs of EAMs (LPGs) showed a decreasing trend since 2016 and rose again in 2019. Overall, the DDDs of EAMs(LPGs) decreased by 25.18% between 2016 and 2020, but the proportion selected for clinical treatment remained at 67.35% in 2020. The DDDs of EAMs (OBs) and IAMs both showed an increasing trend year by year, with a proportional increase of 207.72% and 652.68%, respectively; but the proportion selected for clinical treatment was only 16.09% and 16.56% respectively in 2020. Under the standard set in this study, EAMs (LPGs) had good affordability for urban residents but poor affordability for rural residents; all IAMs were affordable to urban residents, but most IAMs(11/17) were not affordable to rural residents by 2020. However, the affordability of these drugs was constantly improving.Conclusions There were no significant changes in the availability and cost of EAMs (LPGs), whose lower prices showed better affordability, especially for urban residents. Although their relative change in drug utilization showed a decreasing trend, they still dominated clinical treatment. Driven by the national drug price negotiation (NDPN) policy, the availability of IAMs was on the rise. The prices of IAMs and EAMs (OBs) decreased year by year with significantly improving affordability, but the high prices of these drugs remained unaffordable for rural residents. It is necessary to further develop and strengthen policies for essential medicines procurement assessment to improve the accessibility of EAMs. Meanwhile, a comprehensive strategy is needed in the future to improve the affordability of IAMs.