Climate change affects global crop production year after year. Exploring the impact of different fertilization methods on crop yield stability has become an extremely important topic in sustainable agriculture. The objective of this study is to explore the effects of various fertilization regimes with climate variability on yield stability for sweet corn production in southern Taiwan. Three fertilization treatments composed of chemical fertilizer only (CF), integrated fertilizer (half organic/half chemical fertilizer) (IF), and organic fertilizer only (OF) were implemented from 2009 to 2018 based on the well-maintained soils since 1988. While the same amounts of these fertilizers were applied during the period, we found that different fertilization changed the marketable yields of fresh fruit (ear), which slightly increased for organic fertilizer, but substantially decreased for both chemical (p = 0.0001) and integrated (p = 0.0061) fertilizer. Thus, based on these 10 years of observation, yields among fertilization treatments were analyzed with weather and soil parameters to determine the possible factors involved. Both multiple linear regression equation (p < 0.0001, adj. R2 > 0.57) and regression tree analysis illustrated significantly negative correlations between average ear weight and relative humidity under the chemical fertilizer treatment. In this study, we show for the first time that chemical fertilizer had the lowest yield resilience in response to regional relative humidity change compared to organic and integrated fertilizers. Our results also indicate that specific soil microbes have the potential to help sweet corn face environmental vulnerability in subtropical regions.