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The eastern waters of Taiwan have been lacking baseline and research data for several years. This study was initiated by Kuroshio Ocean Education Foundation (KOEF) in collaboration with the Turumoan whale-watching company since 1998, collecting long-term ecological data for cetaceans in the inshore of Hualien, eastern Taiwan. This dataset includes 10,675 records of cetacean sightings from June 1998 to December 2021. Collection of cetacean sighting records was paused for one year in 2001 due to budgetary reasons. All of the sighting records were collected by whale-watching boat guides that were trained by KOEF. Following a standardised protocol, guides used a handheld GPS device and cetacean sighting record sheets to document information about the cetacean species identification, location, time, number of individuals, the presence of mother-calf pairs and mixed-species groups and other states of each sighting during a whale-watching tour. The collection of citizen-science data during this period has significantly advanced Taiwan's cetacean baseline data in the study area. Additionally, we make data available to the public in the form of citizen-science, making a substantial contribution to the advancement of ocean scientific research. We have published the dataset on Global Biodiversity Information Facility, allowing users around the world to download the dataset.This is currently the largest dataset of cetacean sighting records in Taiwan (last updated on 2023-09-05). We have also recorded several species on the International Union for Conservation of Nature (IUCN) Red List categorised as "Data Deficient" during our survey inshore of Hualien, eastern Taiwan, including Ginkgo-toothed beaked whales (Mesoplodon ginkgodens Nishiwaki & Kamiya, 1958), Omura's whales (Balaenoptera omurai Wada, Oishi & Yamada, 2003) and killer whales (Orcinus orca (Linnaeus, 1758)). There are also sperm whales (Physeter macrocephalus Linnaeus, 1758), categorised as "Vulnerable" in the IUCN Red List and false killer whales (Pseudorca crassidens (Owen, 1846)), categorised as "Near Threatened". This study is also the first and only long-term study that has documented cetaceans in the study area.