Agroforestry systems are widely used all over the world, especially in southern Xinjiang, China, because of their multiple ecosystem functioning and services. However, the effects of tree canopy structure on the microenvironment and associated crop yield remain unclear. We set up a field experiment with four tree forms of almonds (Amygdalus communis L.), delayed open-central shape (DC), semicircle small-canopy shape (SC), open-center shape (OC), and high-stem shape (HS), which were intercropped with wheat (Triticum aestivum L.) separately. We measured the wheat yields and the photosynthetically active radiation (PAR), temperature, humidity, and red/far-red light ratio at various intercropped positions (1 m, 2 m, and 3 m apart from tree line). The results showed that wheat yield and yield components were affected jointly by the tree forms and the intercropping position. Compared with monoculture wheat, the yields of intercropped wheat with DC, SC, OC, and HS were decreased by 63.7%, 18.2%, 35.4%, and 33.0%, respectively. Tree form is largely influential to PAR, red light/far-red light, temperature, and humidity in the intercropped areas. The PAR in the intercropped wheat area was SC > HS/OC > DC, and PAR was increased with the distance from the tree line. PAR correlated significantly with R/FR, mean daily temperature, and relative humidity. PAR measured for wheat at various growth and development stages had significant positive correlations with thousand kernel weight, number of spikes, kernel number per spike, and grain yield. The structural equation model revealed that the yields of wheat were affected primarily by the PAR at the flowering and filling stages, with a contribution of up to 68%. Choosing a proper tree form (i.e., SC) and pruning to increase the trunk height or to remove the center pole is important to increase the quantity of light penetration and thereby increase the potential of wheat grain yields.