The driving mechanism of soil quality (SQ) has important implications for arable land protection, sustainable agricultural development and ecological environment conservation. This study builds a “perception–response” theoretical framework to investigate how farmers’ land use behavior may affect SQ from the temporal and spatial perspectives. Based on soil sampling data, farmer survey data and socioeconomic statistical data collected in a typical peri-urban area of northeast China, geo-statistical analysis and econometric models have been applied to examine the effect of farmers’ land use behavior (FLUB) on SQ. The results show that during 1980–2010, the target of FLUB has been shifted from “grain output maximization” to “grain output and profit maximization” and then to “profit maximization”. The FLUB, including land use pattern, land use degree and land input intensity, also show obvious differences in space. These differences result in distinct impacts on the variation of SQ in time and space. Generally, the soil organic matter (OM) tends to decline, the available nitrogen (AVN) and available phosphorus (ANP) tend to rise, while the available potassium (AVK) increases after an initial decline. Moreover, the further distance from the city center, the greater the spatial variation of SQ in space. These findings are not only helpful from a theoretical and practical significance for policy-makers to improve SQ in the outskirts of metropolitan areas, but also make an important contribution to the sustainable development of peri-urban agriculture (PUA).