Extreme climate changes have resulted in poor microalgae proliferation in recent years, resulting in an insufficient supply of live food microalgae available to Taiwan's hard clam (Meretrix lusoria) farming industry. To alleviate the impacts of rapid climate changes on the hard clam farming industry, improve the survival of hard clams, and produce photovoltaic green energy, this experiment used solar photovoltaic panels to cover hard clam culture ponds, enhancing the production efficiency of each pond unit. The hard clam culture ponds were covered with solar photovoltaic panels featuring different shadow ratios, and the temperature changes and diversity of microalgae compositions in the hard clam pond water were measured. The microalgae were collected and separated from the hard clam culture ponds and further tested for high- and low-temperature tolerance and the effectiveness of hard clam cultivation was evaluated. The test results showed that the use of solar photovoltaic panels to cover hard calm cultivation ponds stabilized changes in the water temperature. The maximum difference in water temperatures measured in hard clam ponds without cover was 11.19°C, which was nearly twice the temperature differences measured in the hard clam ponds covered with photovoltaic panels providing 40% and 70% shading. The microalgae collected and separated from the hard clam cultivation ponds displayed better proliferation under high-temperature environments. The highest microalgae cell populations per milliliter were measured in the high-temperature culture, at 434,200 for Coscinodiscus sp., 771,000 for Amphiprora sp., 9.7851 million for Chlorella sp., and 3.7708 million for Chaetoceros sp., which were higher than the populations measured in the low-temperature culture. These results indicated that hard clam ponds could be covered by solar photovoltaic panels to stabilize the cultivation environment, maintain the ecological diversity of the microalgae composition in the water, and produce more diatoms to feed hard clams while simultaneously improving the cultivation efficiency of hard clams.