As global warming increases day/night temperatures as well as frequencies of heat waves, studying physiological responses in long-term heat stress is required for sustainable yield production in the future. In this study, effects of long-term heat stress on photosynthetic, morphological, and yield parameters of three cherry tomato accessions, HR17, HR22, and HR24, were evaluated. The experiment was conducted under two temperature greenhouse conditions, where temperature set-point for ventilation was 30 °C and 35 °C during the day for 57 days, respectively. Plants were harvested on the 35th days and 57th days after heat treatments, and their physiological and morphological characteristics and yield traits were measured. Under control conditions, HR17 and HR22 had 0.5–0.6 harvest index, while HR24 had 0.3 harvest index. On 35th days after heat treatment, although yield loss percentage of HR17 was high (43%), it produced the highest fruit yield among all three accessions. However, after longer heat treatment, HR24 produced the highest fruit yields among all accessions with the smallest yield loss (34%). Furthermore, yield loss was highly associated with reductions in nitrogen use efficiency and water content in plant body under heat stress. The results of this study will provide breeders with a new insight into selecting heat-tolerant genotypes in cherry tomatoes.