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Objectives: To compare the effectiveness of caries arrest by micro-operative treatment (sealing) to operative treatment (flowable resin composite restoration) through a 2-year randomized controlled clinical trial. Materials and methods: A prospective randomized controlled trial was conducted among 7-9-year-old children. At baseline, 630 subjects were screened and 92 children who had at least one carious lesion classified as ICDAS 3 on the pit and fissure of first permanent molar were included. Then they were randomly assigned to the sealant group (73 lesions) and the flowable resin composite group (76 lesions) to receive the corresponding intervention. Lesions status in each group was evaluated every 6 months up to 24 months. Clinical progression of dental caries and materials retention were the outcomes used for group comparisons at p-value < 0.05. Results: After 24 months, three lesions (4.1%) in the sealant group clinically progressed to dentin caries. No lesion in the flowable composite group was observed a progression. The results of Life-table survival analysis show that the cumulative caries arrest rate had no statistically significant difference between the two groups (p = 0.075). However, the cumulative retention rate was 57.5% in the sealant group and 92.1% in the flowable composite group, with significant differences (p < 0.001). The multilevel mixed model showed the sealant had higher risk of retention failure than the flowable composite (OR = 8.66, p < 0.001), while tooth position did not influence material retention (p = 0.083). In addition, the results of Fisher Exact test show that dentin lesions had more retention failure than enamel lesions in the sealant group (p = 0.026). Conclusion: Although sealing microcavitated carious lesions of the first permanent molar achieved lower retention rate than resin composite restoration, both sealing and restoration effectively arrested caries progression for two years. Clinical relevance: To preserving dental structure and delaying or eliminating the need for operative procedures, microcavitated carious lesion can be arrested by sealing. Trial registration: Registered at ; Feb 15th, 2020; No. ChiCTR2000029862. [ABSTRACT FROM AUTHOR]