Morchella spp. are rare and highly valued edible fungi that often exhibit unstable yield and quality under protected cultivation due to inadequate regulation of the light and temperature microenvironment. Colored films can effectively optimize these conditions. In this study, the effects of six colored film treatments—white film (WM), red film (RM), green film (GM), blue film (BM), black film (BKM), and silver-black film (SBM)—on the microenvironment and development of Morchella septimelata and M. sextelata were investigated. The results showed that the BM treatment improved the microenvironment and promoted Morchella development. BM exhibited high transmittance, enhancing light intensity and increasing accumulated air and soil temperatures. It also led to the production of the greatest number of mature fruiting bodies, with 46 per square meter for M. septimelata and 54 per square meter for M. sextelata. Agronomic traits were also superior under the BM treatment, with pileus lengths of 82.97 mm for M. septimelata and 70.76 mm for M. sextelata. Compared with WM, BM significantly increased the weight of a single fruiting body and yield by 12.23% and 20.86% for M. septimelata and by 18.14% and 25.34% for M. sextelata, respectively. BM also significantly increased crude fiber content by 16.92% in M. septimelata and 2.63% in M. sextelata. RM significantly increased crude polysaccharide content by 47.42% in M. septimelata and by 44.12% in M. sextelata. This study indicated that BM was the preferred choice for Morchella protected cultivation.